|
| Status |
Public on Apr 30, 2022 |
| Title |
TLElab_ChIPseq_antiGafY_Ccres_delta_rogAgafY_replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
Caulobacter crecentus CB15N
|
| Organism |
Caulobacter vibrioides |
| Characteristics |
developmental stage: mixed population, stationary phase
genotype: CB15N delta-rogAdelta-gafY
|
| Treatment protocol |
cells were grown to stationary phase (in PYE at 28 degC) before formadehyde were added to 1% (final concentraation) to fix cells for ChIP-seq.
None
|
| Growth protocol |
Cultures of Caulobacter crescentus were grown at 28oC in PYE and supplemented with antibiotics, as necessary, to either exponential phase (for ChIP-seq of rogA) or to stationary phase (for ChIP-seq of GafY and GafZ). Subsequently, formadehyde (1% final concentration, 30 min) were added to fix cells for ChIP-seq.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using the Qiagen Cell Lysis and Protein Precipitation solutions. Detailed protocols are listed in the Supplementary Materials
Standard library construction for Illumina Hiseq2500 sequencing platform
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
For analysis of ChIP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command:bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage at each nucleotide position was computed using BEDTools (Quinlan and Hall, 2010) using the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. Finally, ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) using custom R scripts.
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Files ending with _coverage.txt: tab-delimited text file of nucleotide-resolution coverage from ChIP-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)
|
| |
|
| Submission date |
Sep 20, 2021 |
| Last update date |
Apr 30, 2022 |
| Contact name |
Kevin Gozzi |
| E-mail(s) |
[email protected]
|
| Phone |
2038153995
|
| Organization name |
Massachusetts Institute of Techonology
|
| Street address |
31 Ames St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL18006 |
| Series (1) |
| GSE184477 |
Gene transfer agents promote survival and DNA repair during stationary phase for Caulobacter crescentus (ChIP-Seq) |
|
| Relations |
| BioSample |
SAMN21526219 |
| SRA |
SRX12268792 |
