|
| Status |
Public on Nov 19, 2016 |
| Title |
ecoli_k12_pBADsigma32I54N_30C_m_2 |
| Sample type |
SRA |
| |
|
| Source name |
E. coli cultures
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
plasmid: pBADsigma32I54N
growth temperature: 30C
induction: 0.2% arabinose
treatment temperature: 30C
heat shock time: None
replicate: 2
|
| Treatment protocol |
Cells were induced with arabinose or heat shocked, then harvested and flash frozen.
|
| Growth protocol |
E. coli were grown in defined rich media at 30C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in liquid nitrogen, then samples were taken for total RNA.
Total RNA was extracted with phenol chloroform and alkaline fragmented, then fragments (20-40 nt) were gel-purified.
RNA was dephosphorylated, ligated to an adaptor, reverse transcribed, circularized then amplified with Illumina adaptors and barcodes.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Total mRNA
Processed data file: ecoli_heatshock_rawcounts.txt
Processed data file: ecoli_heatshock_normalizedcounts.txt
|
| Data processing |
Basecalls performed using Illumina CASAVA.
Reads were trimmed and adaptors removed using the fastx_toolkit.
Reads were aligned to the MG1655 genome with Bowtie.
The number of reads at each position in the genome was counted using in-house Python scripts.
The number of reads mapping to each gene was counted and normalized using EdgeR.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: ecoli_heatshock_rawcounts.txt: Tab-delimited text file has raw read counts per kilobase million for each E. coli gene (EcoCyc gene names).
Supplementary_files_format_and_content: ecoli_heatshock_normalizedcounts.txt: Tab-delimited text file has EdgeR-normalized counts per kilobase million for each E. coli gene (EcoCyc gene names).
|
| |
|
| Submission date |
Nov 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Evan Thomas Powers |
| E-mail(s) |
epowers@scripps.edu
|
| Organization name |
The Scripps Research Institute
|
| Department |
Chemistry
|
| Street address |
10550 North Torrey Pines Rd
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL15010 |
| Series (1) |
| GSE90056 |
Translation efficiency is maintained during heat shock in Escherichia coli |
|
| Relations |
| BioSample |
SAMN06040731 |
| SRA |
SRX2360374 |
