|
| Status |
Public on May 30, 2017 |
| Title |
1H2O2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole cell
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
strain: MG1655
treatment: Bacteria grown for 12 h in M9 + 100 mM H2O2
time: 12 h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial was harvested with 0.5 Vol of 5% Phenol in Ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using Rneasy.
Library constructed using KAPA Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Bacteria grown for 12 h in M9 + 100 mM H2O2
|
| Data processing |
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. Trimmed reads were aligned on most recent reference genome of Escherichia coli (U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). Finally, Cufflink is used to generate FPKM-normalized expression value for each gene.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: vcf, mutations called; fpkm_tracking, fpkm-normalized expression values
|
| |
|
| Submission date |
Jun 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ilias Tagkopoulos |
| E-mail(s) |
iliast@ucdavis.edu
|
| Organization name |
university of california at davis
|
| Street address |
2063 kemper hall, 1 shields avenue
|
| City |
davis |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL15010 |
| Series (1) |
| GSE58325 |
The Genetic and Transcriptional Basis of Short and Long Term Adaptation across Multiple Stresses in Escherichia coli |
|
| Relations |
| BioSample |
SAMN02847852 |
| SRA |
SRX581917 |
