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C. crescentus NA1000
The NA1000 chromosome (RefSeq NC_011916.1, 4,042,929 bp) with its RefSeq annotation and 112 further tracks. Every track says where it came from: experimental tracks link to their GEO record or paper, and computed tracks (motif matches, palindromes, GC) say exactly how they were made. Data built on strain CB15 was mapped to NA1000 genes by identical protein sequence.
Jump to: Origin region · ctrA · dnaA · gcrA · ccrM · popZ · parB · ftsZ · ccnA
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Tracks
Tick a track to load it. Search the browser by gene name or locus tag (for example ctrA or CCNA_03130).
Annotation 5 tracks
Experimentally detected non-coding RNAs (sRNAs, antisense RNAs, tmRNA, 4.5S, RNase P) with literature names (CcnA, ChvR, GsrN, RusT, AbnZ, CrfA, SisA-D). Per-feature sources in srnas.tsv.
source & method
RefSeq NC_011916.1 non-coding RNA features (all EXISTENCE evidence); all 141 Schrader 2014 Dataset S1 ncRNAs matched exactly. Names only from papers stating the CCNA_R tag. tmRNA = span of both fragments. 1-based to BED.
NC_011916.1Schrader et al. 2014download (7 kB)154 features
TSSs mapped by 5' global RACE across the cell cycle. Name = category:CCNA (P primary, I internal, A antisense, N non-coding, IP/AP mixed); ':ccr' = cell-cycle regulated.
source & method
S1 Dataset (pgen.1004831.s011.xlsx), all 2726 rows: 1-based TSS position -> BED [pos-1,pos), strand as given; colored by category. S16 (unverified antisense TSSs) not included.
Zhou et al. 2015download (193 kB)2,726 features
5' UTRs derived from primary TSSs (Zhou 2015) to the start codon of the next same-strand RefSeq CDS, when 1-500 nt. Name = 5UTR:gene:length.
source & method
For TSS categories P/IP/AP: nearest RefSeq CDS start on same strand at/after the TSS; UTR = TSS..start-1 if 1-500 nt. 174 leaderless (TSS=start) and 1 >500 nt skipped. All 1549 hit the CDS Zhou assigned.
NC_011916.1Zhou et al. 2015download (80 kB)1,549 features
Tn-seq essential elements: essential ORFs (red), high-fitness-cost ORFs (orange), essential regulatory regions (blue), essential non-coding elements (purple). Category in name.
source & method
Dataset 1 (msb201158-s2.xls): DT2 ORFs essential/High_Fitness_Costs (3240 nonessential omitted), DT3 regulatory (negative coords = minus strand), DT1 non-coding (no strand). 1-based inclusive -> BED; published coords kept.
Christen et al. 2011download (103 kB)1,168 features
Operon map (multi-CDS transcription units) from ribosome profiling/RNA-seq. Spans first start codon to last stop codon. Name = first-last CDS (n genes).
source & method
Dataset S1 'Operons' sheet: rows grouped by (operon start, stop, strand). Dropped 14 single-CDS groups and 4 groups whose bounds/strand disagree with member CDS coordinates (listed in log.txt).
Schrader et al. 2014download (48 kB)844 features
Expression · microarray 28 tracks
Wild-type CB15N swarmer cells synchronized and released into M2G; RNA at 0 min vs a common asynchronous log-phase reference (two-colour oligo array, 2 replicate arrays). Values: log2 ratio synchronized time point / asynchronous reference.
source & method
Series-matrix VALUEs; GPL1076 CC_ tags→NA1000 genes by sequence lift-over; 16 probes not sense-strand in gene dropped; probe mean per gene per array; per-array sign → test/ref; mean of 2 arrays (gene kept if in ≥50%)
Wild-type CB15N swarmer cells synchronized and released into M2G; RNA at 30 min vs a common asynchronous log-phase reference (two-colour oligo array, 2 replicate arrays). Values: log2 ratio synchronized time point / asynchronous reference.
source & method
Series-matrix VALUEs; GPL1076 CC_ tags→NA1000 genes by sequence lift-over; 16 probes not sense-strand in gene dropped; probe mean per gene per array; per-array sign → test/ref; mean of 2 arrays (gene kept if in ≥50%)
Wild-type CB15N swarmer cells synchronized and released into M2G; RNA at 60 min vs a common asynchronous log-phase reference (two-colour oligo array, 2 replicate arrays). Values: log2 ratio synchronized time point / asynchronous reference.
source & method
Series-matrix VALUEs; GPL1076 CC_ tags→NA1000 genes by sequence lift-over; 16 probes not sense-strand in gene dropped; probe mean per gene per array; per-array sign → test/ref; mean of 2 arrays (gene kept if in ≥50%)
Wild-type CB15N swarmer cells synchronized and released into M2G; RNA at 90 min vs a common asynchronous log-phase reference (two-colour oligo array, 2 replicate arrays). Values: log2 ratio synchronized time point / asynchronous reference.
source & method
Series-matrix VALUEs; GPL1076 CC_ tags→NA1000 genes by sequence lift-over; 16 probes not sense-strand in gene dropped; probe mean per gene per array; per-array sign → test/ref; mean of 2 arrays (gene kept if in ≥50%)
Wild-type CB15N swarmer cells synchronized and released into M2G; RNA at 120 min vs a common asynchronous log-phase reference (two-colour oligo array, 2 replicate arrays). Values: log2 ratio synchronized time point / asynchronous reference.
source & method
Series-matrix VALUEs; GPL1076 CC_ tags→NA1000 genes by sequence lift-over; 16 probes not sense-strand in gene dropped; probe mean per gene per array; per-array sign → test/ref; mean of 2 arrays (gene kept if in ≥50%)
Wild-type CB15N swarmer cells synchronized and released into M2G; RNA at 150 min vs a common asynchronous log-phase reference (two-colour oligo array, 2 replicate arrays). Values: log2 ratio synchronized time point / asynchronous reference.
source & method
Series-matrix VALUEs; GPL1076 CC_ tags→NA1000 genes by sequence lift-over; 16 probes not sense-strand in gene dropped; probe mean per gene per array; per-array sign → test/ref; mean of 2 arrays (gene kept if in ≥50%)
GcrA depletion strain LS3707 (xylose-dependent gcrA) 2 h in PYE+glucose (GcrA depleted) vs PYE+xylose; 7 arrays incl. dye swaps. Values: log2 ratio glucose (GcrA-depleted) / xylose.
source & method
Series-matrix VALUEs; GPL1076 CC_ tags→NA1000 genes by sequence lift-over; 16 probes not sense-strand in gene dropped; probe mean per gene per array; per-array sign → test/ref; mean of 7 arrays (gene kept if in ≥50%)
SciP depletion strain: G1 swarmer cells isolated after one cell cycle in glucose (SciP depleted) vs xylose; 2 arrays. Values: log2 ratio glucose (SciP-depleted) / xylose.
source & method
Series-matrix VALUEs; GPL10469 CC_ tags→NA1000 genes by sequence lift-over; 6269 probes not sense-strand in gene dropped; probe mean per gene per array ×log2(10) (VALUE is log10); mean of 2 arrays (gene kept if in ≥50%); orientation per sample title (glu/xyl); GEO dye labels conflict
Wild type overexpressing sciP (xylose) vs wild type with empty vector (xylose); 2 arrays. Values: log2 ratio sciP overexpression / empty vector.
source & method
Series-matrix VALUEs; GPL10469 CC_ tags→NA1000 genes by sequence lift-over; 6269 probes not sense-strand in gene dropped; probe mean per gene per array ×log2(10) (VALUE is log10); mean of 2 arrays (gene kept if in ≥50%)
NA1000 (LS101) mixed population shifted to M2 without glucose for 30 min vs M2G control; Affymetrix, 2 biological replicates each. Values: log2 ratio (difference of RMA log2 means) M2 / M2G.
source & method
Series-matrix VALUEs; GPL11304 CC_ tags→NA1000 genes by sequence lift-over; probes averaged per gene; mean RMA log2 of 2 test minus mean of 2 reference arrays
NA1000 (LS101) mixed population shifted to M2 without glucose for 60 min vs M2G control; Affymetrix, 2 biological replicates each. Values: log2 ratio (difference of RMA log2 means) M2 / M2G.
source & method
Series-matrix VALUEs; GPL11304 CC_ tags→NA1000 genes by sequence lift-over; probes averaged per gene; mean RMA log2 of 2 test minus mean of 2 reference arrays
ΔphoU Pvan-phoU strain 7 h without vanillate (PhoU depleted) vs with vanillate, PYE; 2 array(s). Values: log2 ratio -vanillate (PhoU-depleted) / +vanillate.
source & method
Series-matrix VALUEs; GPL15487 CCNA_ tags; 16 probes not sense-strand in gene dropped; probe mean per gene per array ×log2(10) (VALUE is log10); mean of 2 arrays (gene kept if in ≥50%)
ΔphoU Pvan-phoU strain 16 h without vanillate (PhoU depleted) vs with vanillate, PYE; 1 array(s). Values: log2 ratio -vanillate (PhoU-depleted) / +vanillate.
source & method
Series-matrix VALUEs; GPL15487 CCNA_ tags; 16 probes not sense-strand in gene dropped; probe mean per gene per array ×log2(10) (VALUE is log10); mean of 1 arrays (gene kept if in ≥50%)
NA1000 wild type under iron limitation (2,2-dipyridyl) vs iron-replete; 2 arrays. Values: log2 ratio dipyridyl / iron-replete.
source & method
Series-matrix VALUEs; GPL10469 CC_ tags→NA1000 genes by sequence lift-over; 6269 probes not sense-strand in gene dropped; probe mean per gene per array ×log2(10) (VALUE is log10); mean of 2 arrays (gene kept if in ≥50%)
Δfur mutant vs wild type, both iron-replete; 2 arrays. Values: log2 ratio Δfur / wild type.
source & method
Series-matrix VALUEs; GPL10469 CC_ tags→NA1000 genes by sequence lift-over; 6269 probes not sense-strand in gene dropped; probe mean per gene per array ×log2(10) (VALUE is log10); mean of 2 arrays (gene kept if in ≥50%)
NA1000 ΔccrM (no GANTC methylation) vs wild type; NimbleGen, 3 biological replicates each. Values: log2 ratio (difference of RMA log2 means) ΔccrM / wild type.
source & method
Series-matrix VALUEs; GPL17931 CCNA_ tags; probes averaged per gene; mean RMA log2 of 3 test minus mean of 3 reference arrays
Absolute expression in wild-type NA1000 mixed population (3 NimbleGen arrays): mean RMA log2 signal; compares genes within this track only. Values: log2 normalized signal (RMA).
source & method
Series-matrix VALUEs; GPL17931 CCNA_ tags; mean RMA log2 of 3 arrays
NA1000 ΔcdnL (CarD-like RNAP regulator) vs wild type; NimbleGen, 3 biological replicates each. Values: log2 ratio (difference of RMA log2 means) ΔcdnL / wild type.
source & method
Series-matrix VALUEs; GPL17931 CCNA_ tags; probes averaged per gene; mean RMA log2 of 3 test minus mean of 3 reference arrays
ΔsigT vs wild type, both under sucrose (hyperosmotic) stress; 3 arrays. Shows the σT-dependent general stress response. Values: log2 ratio ΔsigT / wild type.
source & method
Series-matrix VALUEs; GPL10469 CC_ tags→NA1000 genes by sequence lift-over; 6269 probes not sense-strand in gene dropped; probe mean per gene per array ×log2(10) (VALUE is log10); mean of 3 arrays (gene kept if in ≥50%)
ΔphyR vs wild type, both under sucrose (hyperosmotic) stress; 3 arrays. Shows the PhyR-dependent general stress response. Values: log2 ratio ΔphyR / wild type.
source & method
Series-matrix VALUEs; GPL10469 CC_ tags→NA1000 genes by sequence lift-over; 6269 probes not sense-strand in gene dropped; probe mean per gene per array ×log2(10) (VALUE is log10); mean of 3 arrays (gene kept if in ≥50%)
NA1000 under hyperosmotic sucrose stress vs unstressed; 3 arrays. Values: log2 ratio sucrose / no stress.
source & method
Series-matrix VALUEs; GPL14163 CC_ tags→NA1000 genes by sequence lift-over; 4460 probes not sense-strand in gene dropped; probe mean per gene per array ×log2(10) (VALUE is log10); mean of 3 arrays (gene kept if in ≥50%)
NA1000 under hyperosmotic NaCl stress vs unstressed; 3 arrays. Values: log2 ratio NaCl / no stress.
source & method
Series-matrix VALUEs; GPL14163 CC_ tags→NA1000 genes by sequence lift-over; 4460 probes not sense-strand in gene dropped; probe mean per gene per array ×log2(10) (VALUE is log10); mean of 3 arrays (gene kept if in ≥50%)
Wild-type NA1000 stationary phase vs log phase; 2 arrays. Values: log2 ratio stationary / log phase.
source & method
Series-matrix VALUEs; GPL10469 CC_ tags→NA1000 genes by sequence lift-over; 6269 probes not sense-strand in gene dropped; probe mean per gene per array ×log2(10) (VALUE is log10); mean of 2 arrays (gene kept if in ≥50%)
ΔcspC (cold-shock protein) vs wild type in stationary phase; 3 arrays. Values: log2 ratio ΔcspC / wild type.
source & method
Series-matrix VALUEs; GPL10469 CC_ tags→NA1000 genes by sequence lift-over; 6269 probes not sense-strand in gene dropped; probe mean per gene per array ×log2(10) (VALUE is log10); mean of 3 arrays (gene kept if in ≥50%)
zur (zinc uptake regulator) mutant vs wild type, both 1 h with 200 µM ZnCl2; 3 arrays. Values: log2 ratio zur mutant / wild type.
source & method
Series-matrix VALUEs; GPL10469 CC_ tags→NA1000 genes by sequence lift-over; 6269 probes not sense-strand in gene dropped; probe mean per gene per array ×log2(10) (VALUE is log10); mean of 3 arrays (gene kept if in ≥50%)
Log-phase cells treated 30 min with NONOate (nitric-oxide donor) vs untreated; 3 arrays incl. dye swap. Values: log2 ratio NONOate-treated / untreated.
source & method
Series-matrix VALUEs; GPL10146 CC_ tags→NA1000 genes by sequence lift-over; 14 probes not sense-strand in gene dropped; probe mean per gene per array; mean of 3 arrays (gene kept if in ≥50%)
Cells grown with nitrate vs ammonium as nitrogen source; 4 arrays incl. dye swaps. Values: log2 ratio nitrate / ammonium.
source & method
Series-matrix VALUEs; GPL1076 CC_ tags→NA1000 genes by sequence lift-over; 16 probes not sense-strand in gene dropped; probe mean per gene per array; per-array sign → test/ref; mean of 4 arrays (gene kept if in ≥50%)
CB15N growing exponentially in M2-inositol vs M2-glucose; 2 arrays (dye swap). Values: log2 ratio inositol / glucose.
source & method
Series-matrix VALUEs; GPL2749 CC_ tags→NA1000 genes by sequence lift-over; 13 probes not sense-strand in gene dropped; probe mean per gene per array; mean of 2 arrays (gene kept if in ≥50%)
Expression · RNA-seq 15 tracks
Per-gene RNA-seq expression in synchronized NA1000 (M2G, 30 °C) at the swarmer stage; authors' normalized coverage, mean of 3 biological replicates (SOLiD). Values: log2(normalized gene coverage + 1).
source & method
GEO supplementary GSE46915_Caulobacter_CC.csv.gz (authors' per-gene normalized coverage, CP001340 CCNA_ IDs); mean of replicates sw1,sw2,sw3; log2(x+1); drawn over NC_011916.1 gene span.
Per-gene RNA-seq expression in synchronized NA1000 (M2G, 30 °C) at the stalked stage; authors' normalized coverage, mean of 3 biological replicates (SOLiD). Values: log2(normalized gene coverage + 1).
source & method
GEO supplementary GSE46915_Caulobacter_CC.csv.gz (authors' per-gene normalized coverage, CP001340 CCNA_ IDs); mean of replicates st1,st2,st3; log2(x+1); drawn over NC_011916.1 gene span.
Per-gene RNA-seq expression in synchronized NA1000 (M2G, 30 °C) at the early predivisional stage; authors' normalized coverage, mean of 3 biological replicates (SOLiD). Values: log2(normalized gene coverage + 1).
source & method
GEO supplementary GSE46915_Caulobacter_CC.csv.gz (authors' per-gene normalized coverage, CP001340 CCNA_ IDs); mean of replicates epd1,epd2,epd3; log2(x+1); drawn over NC_011916.1 gene span.
Per-gene RNA-seq expression in synchronized NA1000 (M2G, 30 °C) at the predivisional stage; authors' normalized coverage, mean of 3 biological replicates (SOLiD). Values: log2(normalized gene coverage + 1).
source & method
GEO supplementary GSE46915_Caulobacter_CC.csv.gz (authors' per-gene normalized coverage, CP001340 CCNA_ IDs); mean of replicates pd1,pd2,pd3; log2(x+1); drawn over NC_011916.1 gene span.
Per-gene RNA-seq expression in synchronized NA1000 (M2G, 30 °C) at the late predivisional stage; authors' normalized coverage, mean of 3 biological replicates (SOLiD). Values: log2(normalized gene coverage + 1).
source & method
GEO supplementary GSE46915_Caulobacter_CC.csv.gz (authors' per-gene normalized coverage, CP001340 CCNA_ IDs); mean of replicates lpd1,lpd2,lpd3; log2(x+1); drawn over NC_011916.1 gene span.
RNA-seq read coverage (each read spread over its full length), + strand. NA1000 mixed population, mid-log (OD600 0.5) in M2G, 28 °C. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1326108_M2G_RNA_ME.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (95% of in-gene signal on the gene strand).
RNA-seq read coverage (each read spread over its full length), - strand. NA1000 mixed population, mid-log (OD600 0.5) in M2G, 28 °C. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1326108_M2G_RNA_ME.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (95% of in-gene signal on the gene strand).
RNA-seq read coverage (each read spread over its full length), + strand. NA1000 mixed population, mid-log (OD600 0.5) in PYE, 28 °C. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1326109_PYE_RNA_ME.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (95% of in-gene signal on the gene strand).
RNA-seq read coverage (each read spread over its full length), - strand. NA1000 mixed population, mid-log (OD600 0.5) in PYE, 28 °C. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1326109_PYE_RNA_ME.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (95% of in-gene signal on the gene strand).
RNA-seq 5′-end read density (each read counted at its 5′-most base), + strand. NA1000 synchronized (Ludox) and released in M2G; swarmer sample. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1665588_swarmer_RNA.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (94% of in-gene signal on the gene strand).
RNA-seq 5′-end read density (each read counted at its 5′-most base), - strand. NA1000 synchronized (Ludox) and released in M2G; swarmer sample. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1665588_swarmer_RNA.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (94% of in-gene signal on the gene strand).
RNA-seq 5′-end read density (each read counted at its 5′-most base), + strand. NA1000 synchronized (Ludox) and released in M2G; late stalked sample. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1665590_late_stalk_RNA.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (94% of in-gene signal on the gene strand).
RNA-seq 5′-end read density (each read counted at its 5′-most base), - strand. NA1000 synchronized (Ludox) and released in M2G; late stalked sample. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1665590_late_stalk_RNA.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (94% of in-gene signal on the gene strand).
RNA-seq 5′-end read density (each read counted at its 5′-most base), + strand. NA1000 synchronized (Ludox) and released in M2G; late predivisional sample. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1665592_late_prediv_RNA.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (93% of in-gene signal on the gene strand).
RNA-seq 5′-end read density (each read counted at its 5′-most base), - strand. NA1000 synchronized (Ludox) and released in M2G; late predivisional sample. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1665592_late_prediv_RNA.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (93% of in-gene signal on the gene strand).
Translation 10 tracks
Ribosome-footprint density (footprint centre residues, length-weighted, per GEO), + strand. NA1000 mixed population, mid-log (OD600 0.5) in M2G, 28 °C. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1326110_M2G_RP.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (99% of in-gene signal on the gene strand).
Ribosome-footprint density (footprint centre residues, length-weighted, per GEO), - strand. NA1000 mixed population, mid-log (OD600 0.5) in M2G, 28 °C. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1326110_M2G_RP.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (99% of in-gene signal on the gene strand).
Ribosome-footprint density (footprint centre residues, length-weighted, per GEO), + strand. NA1000 mixed population, mid-log (OD600 0.5) in PYE, 28 °C. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1326111_PYE_RP.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (99% of in-gene signal on the gene strand).
Ribosome-footprint density (footprint centre residues, length-weighted, per GEO), - strand. NA1000 mixed population, mid-log (OD600 0.5) in PYE, 28 °C. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1326111_PYE_RP.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (99% of in-gene signal on the gene strand).
Ribosome-footprint density (footprint centre residues, length-weighted, per GEO), + strand. NA1000 synchronized (Ludox) and released in M2G; swarmer sample. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1665594_swarmer_RP.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (99% of in-gene signal on the gene strand).
Ribosome-footprint density (footprint centre residues, length-weighted, per GEO), - strand. NA1000 synchronized (Ludox) and released in M2G; swarmer sample. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1665594_swarmer_RP.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (99% of in-gene signal on the gene strand).
Ribosome-footprint density (footprint centre residues, length-weighted, per GEO), + strand. NA1000 synchronized (Ludox) and released in M2G; late stalked sample. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1665596_late_stalk_RP.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (99% of in-gene signal on the gene strand).
Ribosome-footprint density (footprint centre residues, length-weighted, per GEO), - strand. NA1000 synchronized (Ludox) and released in M2G; late stalked sample. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1665596_late_stalk_RP.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (99% of in-gene signal on the gene strand).
Ribosome-footprint density (footprint centre residues, length-weighted, per GEO), + strand. NA1000 synchronized (Ludox) and released in M2G; late predivisional sample. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1665598_late_prediv_RP.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (99% of in-gene signal on the gene strand).
Ribosome-footprint density (footprint centre residues, length-weighted, per GEO), - strand. NA1000 synchronized (Ludox) and released in M2G; late predivisional sample. Values: mean read weight per nt in 50-bp bin (raw GEO units, not depth-normalized).
source & method
GEO supplementary GSM1665598_late_prediv_RP.txt.gz (pos, strand, read weight on CP001340 = NC_011916.1, 1-based; rRNA/tRNA/ncRNA reads excluded by authors); summed per 50-bp bin ÷ 50; zero bins omitted; strand as given by GEO (99% of in-gene signal on the gene strand).
Binding · ChIP 42 tracks
CtrA-enriched regions in mid-log NA1000 (anti-CtrA ChIP-seq), as listed by the authors. Values: max % of total reads in a 50-bp probe (in name); score scaled 0-1000.
source & method
Authors' SeqMonk/in-house enriched 50-bp probes (ANNO + NO-ANNO sheets) from GEO xls; 1-based probes -> BED; abutting probes merged; name = associated genes + max %reads; BED score = 1000*value/max.
GSE52849 (GSM1277021)Fumeaux et al. 2014download (4 kB)295 features
SciP-enriched regions in mid-log NA1000 (anti-SciP ChIP-seq), as listed by the authors. Values: max % of total reads in a 50-bp probe (in name); score scaled 0-1000.
source & method
Authors' SeqMonk/in-house enriched 50-bp probes (ANNO + NO-ANNO sheets) from GEO xls; 1-based probes -> BED; abutting probes merged; name = associated genes + max %reads; BED score = 1000*value/max.
GSE52849 (GSM1277022)Fumeaux et al. 2014download (5 kB)331 features
FlbD (sigma54 enhancer-binding protein) enriched regions in NA1000, as listed by the authors. Values: max % of total reads in a 50-bp probe (in name); score scaled 0-1000.
source & method
Authors' SeqMonk/in-house enriched 50-bp probes (ANNO + NO-ANNO sheets) from GEO xls; 1-based probes -> BED; abutting probes merged; name = associated genes + max %reads; BED score = 1000*value/max.
GSE52849 (GSM1277023)Fumeaux et al. 2014download (1 kB)21 features
MucR1-enriched regions in mid-log NA1000 (anti-MucR1 ChIP-seq), as listed by the authors. Values: max % of total reads in a 50-bp probe (in name); score scaled 0-1000.
source & method
Authors' SeqMonk/in-house enriched 50-bp probes (ANNO + NO-ANNO sheets) from GEO xls; 1-based probes -> BED; abutting probes merged; name = associated genes + max %reads; BED score = 1000*value/max.
GSE52849 (GSM1277024)Fumeaux et al. 2014download (3 kB)160 features
MucR2-enriched regions in mid-log NA1000 (anti-MucR2 ChIP-seq), as listed by the authors. Values: max % of total reads in a 50-bp probe (in name); score scaled 0-1000.
source & method
Authors' SeqMonk/in-house enriched 50-bp probes (ANNO + NO-ANNO sheets) from GEO xls; 1-based probes -> BED; abutting probes merged; name = associated genes + max %reads; BED score = 1000*value/max.
GSE52849 (GSM1277025)Fumeaux et al. 2014download (3 kB)225 features
MACS2 CtrA ChIP-seq peaks (q<0.05) in WT NA1000, exponential phase (GHA-490). Includes weak peaks; filter by FE. Values: fold enrichment and -log10 q (in name); summit as thick part.
source & method
Authors' MACS2 peak table (q<0.05) from GEO xlsx; 1-based start -> 0-based BED; thickStart/thickEnd = summit; name = peak id, fold enrichment, -log10 q; BED score = 1000*FE/max.
GSE134017 (GSM3933392)Delaby et al. 2019download (56 kB)2,812 features
MACS2 CtrA ChIP-seq peaks (q<0.05) in WT NA1000, stationary phase (GHA-491). Includes weak peaks; filter by FE. Values: fold enrichment and -log10 q (in name); summit as thick part.
source & method
Authors' MACS2 peak table (q<0.05) from GEO xlsx; 1-based start -> 0-based BED; thickStart/thickEnd = summit; name = peak id, fold enrichment, -log10 q; BED score = 1000*FE/max.
GSE134017 (GSM3933396)Delaby et al. 2019download (58 kB)2,972 features
GcrA-3xFLAG (native promoter) anti-FLAG ChIP-seq, NA1000 in PYE. Values: reads per million (authors' MACS pileup, Gaussian-smoothed), mean per 50 bp.
source & method
Authors' 10-bp wig (MACS 1.4.2 pileup, d=200, Gaussian smoothed, RPM). First data row was glued to the header line and recovered; 13 rows past genome end dropped; mean of five 10-bp bins per 50-bp bin.
GSE73925 (GSM1906338)Haakonsen et al. 2015download (570 kB)80,265 features
RpoC-3xFLAG (RNA polymerase beta') anti-FLAG ChIP-seq, NA1000 in PYE. Values: reads per million (authors' smoothed pileup), mean per 50 bp.
source & method
Authors' 10-bp wig (MACS 1.4.2 pileup, Gaussian smoothed, RPM); 13 rows past genome end dropped; mean of five 10-bp bins per 50-bp bin.
GSE73925 (GSM1906339)Haakonsen et al. 2015download (586 kB)80,226 features
Anti-RpoD (sigma70) ChIP-seq in wild-type NA1000, PYE. Values: reads per million (authors' smoothed pileup), mean per 50 bp.
source & method
Authors' 10-bp wig (MACS 1.4.2 pileup, Gaussian smoothed, RPM); 13 rows past genome end dropped; mean of five 10-bp bins per 50-bp bin.
GSE73925 (GSM1906343)Haakonsen et al. 2015download (597 kB)80,339 features
Sigma32-3xFLAG anti-FLAG ChIP-seq in rifampicin-treated cells (traps RNAP at promoters). Values: reads per million (authors' smoothed pileup), mean per 50 bp.
source & method
Authors' 10-bp wig (MACS 1.4.2 pileup, Gaussian smoothed, RPM); 13 rows past genome end dropped; mean of five 10-bp bins per 50-bp bin.
GSE73925 (GSM1906341)Haakonsen et al. 2015download (572 kB)80,258 features
Sigma54-3xFLAG anti-FLAG ChIP-seq in rifampicin-treated cells. Values: reads per million (authors' smoothed pileup), mean per 50 bp.
source & method
Authors' 10-bp wig (MACS 1.4.2 pileup, Gaussian smoothed, RPM); 13 rows past genome end dropped; mean of five 10-bp bins per 50-bp bin.
GSE73925 (GSM1906342)Haakonsen et al. 2015download (561 kB)80,255 features
Anti-ParB ChIP-seq in wild-type CB15N (NA1000), exponential phase; ParB spreads ~10 kb around parS near the origin. Values: ChIP coverage / genome-wide mean coverage (fold), mean per 50 bp.
source & method
Authors' per-nucleotide ChIP coverage (bowtie -m 1, bedtools; chrom 'CB15N' = NC_011916.1) -> mean per 50-bp bin, divided by the genome-wide per-base mean (1 = genome average). Raw counts, so normalised to genome mean rather than RPM (read totals not given).
GSE100233 (GSM2675528)Tran et al. 2017download (582 kB)79,954 features
Anti-FLAG ChIP-seq of FLAG-SMC (delta-smc, Pxyl-flag-smc plasmid; strain TLS1599). SMC enrichment is weak; see the 1-kb ratio track. Values: ChIP coverage / genome-wide mean coverage (fold), mean per 50 bp.
source & method
Authors' per-nucleotide ChIP coverage (strain TLS1599 per paper Table S1) -> mean per 50-bp bin, divided by the genome-wide per-base mean (1 = genome average). Raw counts, so normalised to genome mean rather than RPM (read totals not given).
GSE97330 (GSM2561777)Tran et al. 2017download (554 kB)79,790 features
FLAG-SMC ChIP divided by untagged-WT anti-FLAG ChIP in 1-kb bins, as in the paper's Fig 3A; peaks at parS near the origin. Values: ratio of read-depth fractions (FLAG-SMC / untagged control) per 1 kb.
source & method
Per-nucleotide coverage of FG_TLS1599 and FG_WT summed per 1 kb, each divided by its genome total, then ratio. 20 bins with zero control coverage left empty. 1-kb (not 50-bp) bins because the signal is weak.
GSE97330 (GSM2561777, GSM2561782)Tran et al. 2017download (26 kB)4,023 features
GapR-3xFLAG anti-FLAG ChIP-seq, NA1000 exponential phase in PYE; GapR tracks overtwisted (positively supercoiled) DNA. Values: ChIP pileup / genome-wide mean (fold), mean per 50 bp.
source & method
Authors' 1-bp MACS 1.4.2 extended-tag pileup wig; 150 positions past the genome end dropped -> mean per 50-bp bin, divided by the genome-wide per-base mean (1 = genome average). Raw counts, so normalised to genome mean rather than RPM (read totals not given).
GSE100657 (GSM2690550)Guo et al. 2018download (589 kB)80,650 features
MucR1 ChIP-exo enriched promoters at 10/40/70/100 min after synchrony (colour = time). Intervals are authors' promoter windows (-500..+100 of gene start), not summits. Values: enrichment ratio (in name, with time and gene); score scaled 0-1000.
source & method
Four GEO ChIP-exo tables (enrichment ratio, from, to, gene) merged; 1-based 'from' -> 0-based start; itemRgb by time point (T10 blue, T40 green, T70 orange, T100 red); score = 1000*ER/max.
GSE79880 (GSM2107771-4)Ardissone et al. 2016download (8 kB)602 features
LexA (SOS repressor) enriched probes in NA1000, max per gene as listed by the authors. Values: max % of total reads in a 50-bp probe (in name); score scaled 0-1000.
source & method
Authors' SeqMonk/in-house enriched 50-bp probes (ANNO + NO-ANNO sheets) from GEO xls; 1-based probes -> BED; abutting probes merged; name = associated genes + max %reads; BED score = 1000*value/max.
GSE76721 (GSM2036554)Kirkpatrick et al. 2016download (1 kB)64 features
HigA (antitoxin of the DNA-damage-inducible HigBA system) enriched probes in NA1000, as listed by the authors. Values: max % of total reads in a 50-bp probe (in name); score scaled 0-1000.
source & method
Authors' SeqMonk/in-house enriched 50-bp probes (ANNO + NO-ANNO sheets) from GEO xls; 1-based probes -> BED; abutting probes merged; name = associated genes + max %reads; BED score = 1000*value/max.
GSE76721 (GSM2036555)Kirkpatrick et al. 2016download (7 kB)588 features
Anti-HigX ChIP-seq in wild-type NA1000 (SOS-induced membrane-associated transcription factor). Values: 50-bp coverage / genome-wide mean (fold).
source & method
Authors' 50-bp bedGraph (described as RPM, but values average 1758/bin, so treated as unnormalised) divided by its genome-wide mean (1 = average).
GSE310922 (GSM9312241)Brejndal et al. 2026download (565 kB)80,209 features
MACS2 narrowPeak calls (q<0.05) for HigX ChIP-seq in wild-type NA1000. Values: fold enrichment and -log10 q (in name); summit as thick part.
source & method
Authors' MACS2 narrowPeak; coordinates kept (already 0-based); summit = start + offset as thick part; score = 1000*FE/max.
GSE310922 (GSM9312241)Brejndal et al. 2026download (14 kB)596 features
ZitP ChIP-seq enriched probe positions reported for the origin-proximal region only (44 probes) in wild-type NA1000. Values: % of reads per probe (in name, 0.1 resolution); score scaled 0-1000.
source & method
Authors' 'Location, %reads_probe' table. Probe width is not documented, so each location is a 1-bp point (1-based -> 0-based); values not altered.
GSE79918 (GSM2108315)Bergé et al. 2016download (1 kB)44 features
PhoB-3xFLAG anti-FLAG ChIP-seq in phosphate-limited M5G medium (PhoB active). Values: pileup / genome-wide mean (fold), mean per 50 bp.
source & method
Authors' 10-bp MACS pileup wig (read counts); 16 rows past genome end dropped -> mean per 50-bp bin, divided by the genome-wide per-base mean (1 = genome average). Raw counts, so normalised to genome mean rather than RPM (read totals not given).
GSE71860 (GSM1847008)Lubin et al. 2016download (524 kB)78,674 features
Anti-UzcR ChIP-seq in wild-type NA1000 exposed to 40 uM ZnSO4 for 1 h. Values: signal / genome-wide mean (fold), mean per 50 bp.
source & method
Authors' 1-bp QuEST/MochiView wig (units undocumented; replicate average) -> mean per 50-bp bin, divided by the genome-wide per-base mean (1 = genome average). Raw counts, so normalised to genome mean rather than RPM (read totals not given).
GSE87171 (GSM2323851)Park et al. 2017download (557 kB)79,699 features
DriD-3xFLAG anti-FLAG ChIP-seq after zeocin DNA damage (SOS-independent damage response activator). Values: read depth / genome-wide mean (fold), mean per 50 bp.
source & method
Authors' wig of raw per-base counts (chrom CB15N, 0-based positions 0..4042928) -> mean per 50-bp bin, divided by the genome-wide per-base mean (1 = genome average). Raw counts, so normalised to genome mean rather than RPM (read totals not given).
GSE197978 (GSM5935095)Gozzi et al. 2022download (559 kB)78,907 features
3xFLAG-NtrC anti-FLAG ChIP-seq vs input, PYE log phase. Values: log2(ChIP/input) as provided by authors, mean per 50 bp.
source & method
Authors' bigWig (log2 output/input, chrom CP001340 = NC_011916.1, sequence verified identical) decoded with a minimal bigWig reader; mean of covered bases per 50-bp bin.
GSE234096North et al. 2023download (626 kB)80,859 features
RedN-Venus ChIP-seq, asynchronous NA1000 culture (replicate 1). Values: per-base coverage per million mapped reads (authors), mean per 50 bp.
source & method
Authors' per-base RPM bedGraph (chrom 'chr1', 1-based positions 1..4042928; final base absent) averaged per 50-bp bin; values unchanged otherwise.
GSE85344 (GSM2265434)Arias‐Cartin et al. 2016download (564 kB)80,680 features
Anti-MipZ ChIP-seq in wild-type NA1000 (GHA-28). Values: reads per million per 50-bp window (authors).
source & method
Authors' RPM-normalised 50-bp window profile (GEO xlsx) copied as-is; windows 1-50, 51-100,... -> 0-based bedGraph; identical adjacent values merged.
GSE137346 (GSM4086387)Corrales-Guerrero et al. 2020download (452 kB)75,757 features
Anti-TacA ChIP-seq in wild-type NA1000 (sigma54 enhancer-binding protein controlled by SpmX/DivJ). Values: % of total reads per 50-bp window (authors).
source & method
Authors' Supplementary Data 2 (50-bp windows, '% of total reads') copied as-is; 1-based windows -> 0-based bedGraph; identical adjacent values merged.
GSE85186 (GSM2259919)Janakiraman et al. 2016download (528 kB)79,220 features
Anti-CdnL ChIP-seq in wild-type NA1000 grown in M2 + glucose (AIYT-335). Values: reads per million per 50-bp window (authors).
source & method
Authors' RPM-normalised 50-bp window profile (GEO xlsx) copied as-is; windows 1-50, 51-100,... -> 0-based bedGraph; identical adjacent values merged.
GSE249185 (GSM7927858)Smith et al. 2024download (565 kB)79,660 features
Anti-TipR ChIP-seq in wild-type NA1000, PYE (AIYT-244). Values: reads per million per 50-bp window (authors).
source & method
Authors' RPM-normalised 50-bp window profile (GEO xlsx) copied as-is; windows 1-50, 51-100,... -> 0-based bedGraph; identical adjacent values merged.
GSE225487 (GSM7049355)Costafrolaz et al. 2023download (512 kB)79,188 features
Anti-HA ChIP-seq of xylose-induced HA-ChvI in NA1000 delta-bla (ADPB-66). Values: reads per million per 50-bp window (authors).
source & method
Authors' RPM-normalised 50-bp window profile (GEO xlsx) copied as-is; windows 1-50, 51-100,... -> 0-based bedGraph; identical adjacent values merged.
GSE309018 (GSM9258338)Costafrolaz et al. 2026download (540 kB)79,421 features
Anti-HA ChIP-seq of NtrX-HA (strain CB15 ntrX::ntrX-HA; profile reported on NA1000 coordinates). Values: reads per million per 50-bp window (authors).
source & method
Authors' RPM-normalised 50-bp window profile (GEO xlsx) copied as-is; windows 1-50, 51-100,... -> 0-based bedGraph; identical adjacent values merged.
GSE247928 (GSM7903192)Vogt et al. 2024download (526 kB)79,359 features
Anti-RogA ChIP-seq in wild-type CB15N, stationary phase (replicate 1); RogA represses the gene transfer agent activators. Values: ChIP coverage / genome-wide mean (fold), mean per 50 bp.
source & method
Authors' per-nucleotide ChIP coverage (bowtie -m 1, bedtools) -> mean per 50-bp bin, divided by the genome-wide per-base mean (1 = genome average). Raw counts, so normalised to genome mean rather than RPM (read totals not given).
GSE184477 (GSM5589677)Gozzi et al. 2022download (563 kB)79,931 features
MACS2 TrcR ChIP-seq peaks (q<0.05) in wild-type NA1000, PYE. Values: fold enrichment, closest gene, -log10 q (in name); summit as thick part.
source & method
Authors' MACS2 peak table (q<0.05) from GEO xlsx; 1-based start -> 0-based BED; thickStart/thickEnd = summit; name = peak id, fold enrichment, -log10 q; BED score = 1000*FE/max.
GSE148652 (GSM4476143)Delaby et al. 2021download (31 kB)1,119 features
MACS2 OpaA ChIP-seq peaks (q<0.05), NA1000 replicate 1 (nucleoid-associated protein). Values: fold enrichment, closest CDS, -log10 q (in name); summit as thick part.
source & method
Authors' MACS2 peak table (q<0.05) from GEO xlsx; 1-based start -> 0-based BED; thickStart/thickEnd = summit; name = peak id, fold enrichment, -log10 q; BED score = 1000*FE/max.
GSE95535 (GSM2516003)Taylor et al. 2017download (31 kB)1,189 features
KdpE ChIP-seq peaks in wild-type cells in M2G with 0.025 mM K+ (authors' table). Values: reads and normalised reads (in name); summit as thick part.
source & method
Authors' peak table (Start/End/Summit coords, reads, normalised reads, flanking genes); 1-based start -> 0-based; score = 1000*normalised reads/max.
GSE253227 (GSM8381837)Quintero-Yanes et al. 2024download (1 kB)20 features
Genrich peaks (q<0.05) for RtrA-3xFLAG ChIP-seq (strain CB15, mapped to NA1000 CP001340). Values: Genrich AUC and -log10 q (in name); summit as thick part.
source & method
Authors' Genrich encodePeak; chrom CP001340 renamed (sequence verified identical to NC_011916.1); summit = start + offset; score = 1000*AUC/max.
GSE241053McLaughlin et al. 2023download (32 kB)1,294 features
Genrich peaks (q<0.05) for RtrB-3xFLAG ChIP-seq (strain CB15, mapped to NA1000 CP001340). Values: Genrich AUC and -log10 q (in name); summit as thick part.
source & method
Authors' Genrich encodePeak; chrom CP001340 renamed (sequence verified identical to NC_011916.1); summit = start + offset; score = 1000*AUC/max.
GSE241053McLaughlin et al. 2023download (17 kB)691 features
Genrich peaks (q<0.05) for CdxA-3xFLAG ChIP-seq (strain CB15, mapped to NA1000 CP001340). Values: Genrich AUC and -log10 q (in name); summit as thick part.
source & method
Authors' Genrich encodePeak; chrom CP001340 renamed (sequence verified identical to NC_011916.1); summit = start + offset; score = 1000*AUC/max.
GSE241053McLaughlin et al. 2023download (23 kB)923 features
Genrich peaks (q<0.05) for CdxB-3xFLAG ChIP-seq (strain CB15, mapped to NA1000 CP001340). Values: Genrich AUC and -log10 q (in name); summit as thick part.
source & method
Authors' Genrich encodePeak; chrom CP001340 renamed (sequence verified identical to NC_011916.1); summit = start + offset; score = 1000*AUC/max.
GSE241053McLaughlin et al. 2023download (7 kB)251 features
Genrich peaks (q<0.05) for 3xFLAG-RtrC ChIP-seq (strain CB15, mapped to NA1000 CP001340.1). Values: Genrich AUC and -log10 q (in name); summit as thick part.
source & method
Authors' Genrich encodePeak; chrom CP001340.1 renamed (sequence verified identical to NC_011916.1); summit = start + offset; score = 1000*AUC/max.
GSE201497McLaughlin et al. 2022download (7 kB)297 features
Methylation 6 tracks
GANTC sites reported unmethylated throughout the cell cycle by SMRT sequencing (Table S2, 27) and/or HinfI cloning (Table S3, 14); 4 found by both. Values: evidence (S2/S3/S2+S3) and avg kinetic scores of both adenines (in name); score 1000 = both methods.
source & method
SI PDF text-extracted; adenine pairs (1-based, + and - strand) parsed; each verified as a GANTC motif in NC_011916.1; BED interval = full 5-bp motif. S2 tier: both scores <40 vs both <70 (table footnote).
PMC3845142 (SI Appendix Tables S2-S4)Kozdon et al. 2013download (1 kB)37 features
GANTC sites upstream of TSSs whose activity changes when the site becomes hemimethylated during replication, with the cell-cycle window (5-40/40-60/60-80 min). Values: hemimethylation window, downstream gene(s), TSS (in name).
source & method
Table S4 rows parsed (59); adenine = TSS - distance (+ strand TSS) or |TSS| + distance (- strand); all 70 resulting motifs verified as GANTC in NC_011916.1; BED = 5-bp motif.
PMC3845142 (SI Appendix Tables S2-S4)Kozdon et al. 2013download (1 kB)70 features
Per-adenine m6A methylation probability at all 9,062 GANTC adenines, wild-type NA1000 exponential culture (ONT R9.5, mCaller). Values: PoM: probability of methylation per GANTC adenine as reported (0-1).
source & method
Authors' methylation_calls.tsv (0-based Start/Stop, strand, PoM). Every row verified as a GANTC adenine on the stated strand; written as 1-bp bedGraph intervals; values unchanged.
GSE260848 (GSM8125600)Campbell et al. 2024download (70 kB)9,062 features
REC-seq: HinfI cuts only unmethylated GANTC, so higher score = more unmethylated (hypomethylated) DNA at that site; wild-type NA1000. Values: REC-seq score: 5' read-end counts at the cleaved site (raw, as provided).
source & method
Authors' table (1-based A..T core of each GANTC, score); widened to the 5-bp motif, verified as GANTC; 1 row (pos 1174186) not GANTC in NC_011916.1 dropped; 1 identical duplicate row collapsed.
GSE79880 (GSM2407479)Ardissone et al. 2016download (20 kB)2,591 features
REC-seq hypomethylation scores in a delta-mucR1 delta-mucR2 mutant; compare with WT to see MucR-protected sites. Values: REC-seq score: 5' read-end counts at the cleaved site (raw, as provided).
source & method
Authors' table (1-based A..T core of each GANTC, score); widened to the 5-bp motif; all 1,311 rows verified as GANTC in NC_011916.1; 1 identical duplicate row collapsed.
GSE79880 (GSM2407483)Ardissone et al. 2016download (10 kB)1,310 features
PacBio SMRT m6A calls (ipdSummary) in wild-type NA1000, labelled by motif: GANTC (CcrM), CGACCAG, CGAC(N7)TRGG, other. Values: motif, IPD ratio, methylated fraction, coverage (in name); BED score = identification QV.
source & method
Authors' modifications.gff (1-based); m6A records only (4,505; m4C/unclassified excluded); motif assigned by matching NC_011916.1 around each base; strand kept.
GSE79880 (GSM2107776)Ardissone et al. 2016download (57 kB)4,505 features
Motifs · computed 2 tracks
Matches to the full CtrA binding consensus TTAA-N7-TTAA. Predictions: many matches are not bound, and CtrA also uses weaker half-sites.
source & method
Exact scan for TTAA-N7-TTAA (symmetric, one entry per site).
Ouimet & Marczynski 2000; Spencer et al. 2009download (1 kB)15 features
Matches to the C. crescentus SOS operator, the direct repeat GTTC-N7-GTTC, on both strands. Predictions, not measured LexA binding.
source & method
Exact scan for GTTC-N7-GTTC and its reverse complement.
da Rocha et al. 2008download (5 kB)101 features
Sequence · computed 4 tracks
Every GANTC sequence in the genome, the motif the CcrM methyltransferase methylates on adenine. Sites, not measured methylation states.
source & method
Exact scan for GANTC on the NA1000 sequence; GANTC is its own reverse complement, so each site is listed once.
Zweiger et al. 1994; Kozdon et al. 2013download (152 kB)4,542 features
Perfect inverted repeats in intergenic DNA: stems of 12 bp or more around a 3–20 bp loop. Those followed by a T-run are flagged terminator-like; the rest are candidates for other functions.
source & method
Exhaustive scan of intergenic intervals (between RefSeq genes) for perfect stems ≥12 bp, loops 3–20 bp, extended while perfect; overlapping calls keep the longest stem. Terminator-like: ≥4 T in the 8 bp after (or ≥4 A before, for the minus strand).
download (11 kB)199 features
GC percentage in 1-kb windows. The genome averages about 67% GC; low-GC islands often mark horizontally acquired DNA.
Running sum of (G−C)/(G+C). Its minimum and maximum mark the replication origin and terminus, where the leading strand switches.
source & method
(G−C)/(G+C) in 10-kb windows every 2 kb, summed along the chromosome from position 1.
download (68 kB)2,018 features