|
| Status |
Public on Nov 14, 2023 |
| Title |
LELab_IHF_manuscript_sample_34 |
| Sample type |
SRA |
| |
|
| Source name |
mixed population, stationary phase
|
| Organism |
Caulobacter vibrioides |
| Characteristics |
tissue: mixed population, stationary phase
genotype: delta_rogA rpoC::rpoC-3xflag
treatment: anti-FLAG
|
| Treatment protocol |
None
|
| Growth protocol |
C. crescentus cell cultures (50 mL) were grown in PYE to a stationary phase and fixed with formaldehyde to a final concentration of 1%. When appropriate, media were supplemented with antibiotics at the following concentrations (liquid/solid media for C. crescentus): kanamycin (5/25); spectinomycin (25/100); oxytetracycline (1/2). Fixed cells were incubated at room temperature for 30 min, then quenched with 0.125 M glycine for 15 min. Cells were washed three times with 1x PBS (pH 7.4) and resuspended in 1 mL of buffer 1 (20 mM K-HEPES pH 7.9, 50 mM KCl, 10% glycerol, and Roche EDTA-free protease inhibitors). Subsequently
|
| 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 or NextSeq550 sequencing platform
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
submitter provided name: Caulobacter crecentus CB15N
|
| Data processing |
For analysis of ChIP-seq data, Hiseq 2500 Illumina short reads (50 bp) or NextSeq550 short reads (75bp) 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.
Assembly: NC_011916.1
Supplementary files format and content: Files starting with LeLab_coverage_output_: 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 |
Nov 07, 2023 |
| Last update date |
Nov 14, 2023 |
| Contact name |
Tung Ba Khanh Le |
| E-mail(s) |
[email protected]
|
| Phone |
01603450776
|
| Organization name |
John Innes Centre
|
| Department |
Department of Molecular Microbiology
|
| Lab |
www.tunglelab.org
|
| Street address |
Colney Lane
|
| City |
Norwich |
| State/province |
Norfolk |
| ZIP/Postal code |
NR4 7UH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18006 |
| Series (1) |
| GSE247216 |
Control of a gene transfer agent cluster in Caulobacter crescentus by transcriptional activation and anti-termination |
|
| Relations |
| BioSample |
SAMN38149331 |
| SRA |
SRX22408658 |
