|
| Status |
Public on Jan 18, 2017 |
| Title |
26% rep1 |
| Sample type |
SRA |
| |
|
| Source name |
E. coli culture
|
| Organism |
Escherichia coli |
| Characteristics |
strain: DMS2564 (K-12 derivative)
rpos level: 26%
|
| Growth protocol |
Cells were inoculated from frozen cultures into 5 mL of LB, and grown. 5 µL of this overnight culture was diluted into 5 mL of LB with the appropriate concentration of arabinose, and grown for 20h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified from 200 µL of overnight culture by pelleting and resuspeding in 500 µL of Trizol at 65°C, followed by purification on a column (Direct-Zol, Zymo Research). Samples received two 30-minute DNase treatments using TURBO DNA-free (Ambion) following the manufacturers instructions. RNA samples were then purified on a column (RNA Clean & Concentrator, Zymo Research). Three samples were prepped from each culture and pooled to generate sufficient RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base calls performed with RTA v1.18.5
the first ten base pairs of each read were trimmed using FASTXToolkit 0.0.13.
Reads were mapped using BWA 0.7.5a
The number read pairs mapped to each gene was counted with HTSeq 0.6.1
Supplementary_files_format_and_content: A tab deliminited file with counts for each gene.
|
| |
|
| Submission date |
Oct 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Stoebel |
| E-mail(s) |
stoebel@g.hmc.edu
|
| Organization name |
Harvey Mudd College
|
| Department |
Biology
|
| Street address |
301 Platt Blvd
|
| City |
Claremont |
| State/province |
CA |
| ZIP/Postal code |
91711 |
| Country |
USA |
| |
|
| Platform ID |
GPL14548 |
| Series (1) |
| GSE87856 |
The genome-wide transcriptional response to varying RpoS levels in Escherichia coli. |
|
| Relations |
| BioSample |
SAMN05897896 |
| SRA |
SRX2239192 |
