|
| Status |
Public on Dec 01, 2020 |
| Title |
Bacteroides xylanisolvens D22 glucose 3 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial Total RNA
|
| Organism |
Bacteroides xylanisolvens |
| Characteristics |
strain: D22
carbon source: glucose
|
| Treatment protocol |
Cells were treated with two volumes of RNA Protect (Qiagen) of the original culture volume then frozen at -80C until RNA was extracted
|
| Growth protocol |
Strains were grown to mid-log on 5 mg/ml mucin O-linked glycans or glucose as a sole carbon source in vitro.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy kit and rRNA depleted with Bacteria Ribo-Zero Kit (Epicentre/Illumina)
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 |
Data was analyzed using Arraystar software (DNASTAR, Inc.)
DEseq2 normalization with default parameters
Gene expression in mucin O-linked glycans was compared to gene expression in glucose reference
Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >10-fold and normalized expression level >1%
Genome_build: NZ_ADCK00000000.1, NZ_ACRS00000000.1, NZ_ACGA00000000.2, Ga0011936
Supplementary_files_format_and_content: xslx files include DEseq2 values for each sample
|
| |
|
| Submission date |
Aug 07, 2020 |
| Last update date |
Dec 01, 2020 |
| Contact name |
Eric Martens |
| E-mail(s) |
emartens@umich.edu
|
| Organization name |
University of Michigan
|
| Street address |
1150 W. Medical Center Dr.
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL21072 |
| Series (1) |
| GSE155869 |
RNA-seq of human gut Bacteroides xylanisolvens and Bacteroides ovatus isolates grown on mucin O-linked glycans compared to glucose |
|
| Relations |
| BioSample |
SAMN15759413 |
| SRA |
SRX8908703 |
