|
| Status |
Public on Jun 30, 2024 |
| Title |
STEC_OFF_51, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Shiga toxin-producing Escherichia coli strain FHI96
|
| Organism |
Escherichia coli |
| Characteristics |
strain: FHI96
genotype/variation: STECmod OFF 51reps
presence or absence of methyltransferase: Absent
|
| Growth protocol |
Mid-log cultures in LB broth.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Trizol according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
STEC_OFF_51_2
|
| Data processing |
Illumina bcl2fastq 2.20.0.422 pipeline.
Bowtie aligner (2.3.2) was used to map reads to the Escherichia coli O104-H4 STEC strain 2011C-3493 complete genome; GenBank accession number CP003289.1.
edgeR version 3.18.1 was used to perform differential expression analysis.
Genome_build: Escherichia coli O104-H4 STEC strain 2011C-3493 (CP003289.1).
Supplementary_files_format_and_content: STECmod_gene_counts.txt: Tab-delimited text file includes abundance measurements.
Supplementary_files_format_and_content: STECmod_ON.VS.OFF-all_genes.txt: Tab-delimited text file includes abundance measurements and expression differences STECmod ON 52reps vs. STECmod OFF 51reps.
|
| |
|
| Submission date |
Apr 14, 2019 |
| Last update date |
Jun 30, 2024 |
| Contact name |
John Michael Atack |
| E-mail(s) |
[email protected]
|
| Organization name |
Griffith University
|
| Department |
Institute for Glycomics
|
| Street address |
Gold Coast Campus
|
| City |
Gold Coast |
| State/province |
QLD |
| ZIP/Postal code |
4215 |
| Country |
Australia |
| |
|
| Platform ID |
GPL25368 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN11415325 |
| SRA |
SRX5680327 |
