|
Status |
Public on Feb 05, 2022 |
Title |
wt_1_60J_30min |
Sample type |
SRA |
|
|
Source name |
E. coli cells
|
Organism |
Escherichia coli str. K-12 substr. MG1655 |
Characteristics |
genotype: WT time point: 30min
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Samples were lysed with lysozyme and DNA extraction was performed using Monarch Genomic DNA Purification Kit (NEB). Libraries were prepared with sonication and the CPD-Seq protocol (Mao et. al).
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Library strategy: CPD-Seq Reads aligned using Bowtie, parameters: -S -m1 –seed 123. Samtools was used to split reads based on fwd or rev orientation. Custom scripts were used to produce TT-counts per gene. Genome_build: U00096.3 Supplementary_files_format_and_content: *_TTcounts.csv: TT-counts normalized to seq depth and TT per gene.
|
|
|
Submission date |
Apr 12, 2021 |
Last update date |
Feb 06, 2022 |
Contact name |
Evgeny Nudler |
E-mail(s) |
evgeny.nudler@nyulangone.org
|
Organization name |
NYU Medical Center
|
Street address |
450 E 29th St
|
City |
New York |
State/province |
NY |
ZIP/Postal code |
10016 |
Country |
USA |
|
|
Platform ID |
GPL21117 |
Series (2) |
GSE171969 |
Pervasive transcription-coupled DNA repair in E. coli [CPD-seq] |
GSE171972 |
Pervasive transcription-coupled DNA repair in E. coli |
|
Relations |
BioSample |
SAMN18719467 |
SRA |
SRX10590101 |