|
| Status |
Public on Feb 21, 2022 |
| Title |
21307_RpoA_HS_i5006_DY330_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
DY330
|
| Organism |
Escherichia coli |
| Characteristics |
antibody: TAP-tag: Sigma i5006
strain: DY330
treatment: 6 min heat shock
|
| Treatment protocol |
Cells were crosslinked with formaldehyde to a final concentration of 1.0%.
|
| Growth protocol |
Cells were grown in 50 ml of LB media at 30˚C in a shaking incubator with a starting OD600=0.1, then crosslinked when the final OD600=0.7-0.8.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with IgG antibody.
Libraries were prepared for sequencing using standard Illumina protocols with modifications; Reference paper:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6054642/
ChIP-exo
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
ChIP-exo reads were aligned using bwa-mem with the following settings: -v (1) -T (30) -h (5)
Remove duplicate reads and generate a deduplicated BAM file. using picard MarkDuplicates and samtools
peaks were called using GeneTrack using the parameters -s 5 -e 10 -F 1
Genome_build: W3110
Supplementary_files_format_and_content: gff format
|
| |
|
| Submission date |
Nov 19, 2021 |
| Last update date |
Feb 21, 2022 |
| Contact name |
B. Franklin Pugh |
| E-mail(s) |
fp265@cornell.edu
|
| Organization name |
Cornell University
|
| Street address |
465 Biotechnology Building
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
|
| Platform ID |
GPL21222 |
| Series (1) |
| GSE189206 |
Genome-wide promoter assembly mechanisms in E. coli measured at single base resolution |
|
| Relations |
| BioSample |
SAMN23309322 |
| SRA |
SRX13178120 |
