|
Status |
Public on Feb 21, 2022 |
Title |
21317_RpoC_MHS_i5006_DY330_rep4 |
Sample type |
SRA |
|
|
Source name |
DY330
|
Organism |
Escherichia coli |
Characteristics |
antibody: TAP-tag: Sigma i5006 strain: DY330
|
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 |
SAMN23309308 |
SRA |
SRX13178134 |