|
| Status |
Public on Feb 05, 2022 |
| Title |
WT |
| Sample type |
SRA |
| |
|
| Source name |
E. coli cells
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
genotype: WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were lysed with lysozyme and RNA extraction was performed using Mastpure DNA and RNA extraction kit (lucigen), treated with Turbo DNA Free and rRNA was removed using Ribominus (Thermo Fisher).
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads aligned using Bowtie2, parameters: –quiet, -p 2, -x
Samtools was used to split reads based on fwd or rev orientation.
HTSeq used to produce gene feature count txt files.
Genome_build: U00096.3
Supplementary_files_format_and_content: *genes.txt: Gene feature raw counts (not normalized).
|
| |
|
| 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) |
| GSE171971 |
Pervasive transcription-coupled DNA repair in E. coli [RNA-seq 2] |
| GSE171972 |
Pervasive transcription-coupled DNA repair in E. coli |
|
| Relations |
| BioSample |
SAMN18719546 |
| SRA |
SRX10590144 |
