|
| Status |
Public on Feb 09, 2017 |
| Title |
Strain HS at 2h replicate C |
| Sample type |
SRA |
| |
|
| Source name |
cell
|
| Organism |
Escherichia coli HS |
| Characteristics |
strain: HS
time point: 2h
growth phase: exponential
|
| Growth protocol |
Triplicate Luria broth cultures (37o C) of LF82 and HS were grown with continuous shaking for 2 hours (exponential phase) and 24 h without shaking (stationary phase).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the cells using the RiboPure Bacteria kit (Life Technologies Corp. Carlsbad, CA), following the manufacturer’s protocol.
Two micrograms of RNA was depleted of ribosomal RNA using the RiboMinus Transcriptome Isolation Kit (Life Technologies Corp. Carlsbad, CA). These samples were then used as a template for strand-specific cDNA synthesis
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw sequences were filtered to remove human sequence contamination, remove short reads (< 50 bp), depleted of duplicate reads, and quality trimmed using Trimmomatic (v 0.32). rRNA sequences were identified and culled using SortMe RNA (v1.9)
Raw sequence reads for LF82 and HS were mapped to NCBI reference genomes NC_011993 and NC_009800, respectively using the Burroughs Wheeler aligner (BWA)
Counts for each annotated genomic loci were determined by HTseq-count (version 0.6.1)
Genome_build: genomes NC_011993 and NC_009800
Supplementary_files_format_and_content: txt, raw count for each sample
|
| |
|
| Submission date |
May 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuanhao Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Stony Brook University
|
| Department |
Applied Mathematics and Statistics
|
| Street address |
AMS Department,Stony Brook University
|
| City |
Stony Brook |
| ZIP/Postal code |
11790 |
| Country |
USA |
| |
|
| Platform ID |
GPL20214 |
| Series (1) |
| GSE69020 |
Identification of candidate adherent-invasive E. coli signature transcripts by genomic/transcriptomic analysis |
|
| Relations |
| BioSample |
SAMN03701433 |
| SRA |
SRX1032861 |
