|
| Status |
Public on Feb 05, 2022 |
| Title |
wt_4_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 |
SAMN18719453 |
| SRA |
SRX10590130 |
