|
| Status |
Public on Oct 03, 2017 |
| Title |
wt.rep1.me |
| Sample type |
SRA |
| |
|
| Source name |
cells
|
| Organism |
Escherichia coli |
| Characteristics |
srain: K12 MG1673
growth phase: Mid exponential
genotype: wildtype
|
| Treatment protocol |
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual.
|
| Growth protocol |
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
NEXTflexRapid Directional RNA-Seq library kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2). In the case of Ion torrent data .bam files were converted using BWA.
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1).
Genome_build: Escherichia coli (NC000913.2)
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values)
|
| |
|
| Submission date |
Oct 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Parul Singh |
| E-mail(s) |
singh.parul686@gmail.com
|
| Organization name |
National Centre for Biological Sciences
|
| Lab |
Dr. Aswin Sai Narain
|
| Street address |
GKVK, Bellary Road
|
| City |
Bangalore |
| ZIP/Postal code |
560065 |
| Country |
India |
| |
|
| Platform ID |
GPL21222 |
| Series (2) |
| GSE104504 |
Crosstalk between global regulators CRP and FIS in E. coli. |
| GSE104505 |
CRP and FIS |
|
| Relations |
| BioSample |
SAMN07730992 |
| SRA |
SRX3238210 |
