|
| Status |
Public on Sep 01, 2020 |
| Title |
Bacteroides xylanisolvens 18002P Porphyran 2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial Total RNA
|
| Organism |
Bacteroides xylanisolvens |
| Characteristics |
strain: 18002P
carbon source: Porphyran
|
| Treatment protocol |
Cells were centrifuged to remove negatively charged polysaccharides and cell pellets 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 seaweed polysaccharides (carrageenan, agarose and/or poprhyran respective to strain) or galactose as a sole carbon source in vitro.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Rneasy kit and rRNA depleted with Microbe Express Kit (Thermo Fisher)
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 |
| |
|
| Description |
Bxylanisolvens18002P DEseq
104697_GGCTAC_S18_L004_R1_001
|
| Data processing |
Data was analyzed using Arraystar software (DNASTAR, Inc.)
DEseq2 normalization with default parameters
Gene expression in seaweed polysaccharides was compared to gene expression in galactose reference
Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >10-fold and with both biological replicates with a normalized expression level >1%
Genome_build: B. thetaiotaomicron 3731 is NZ_CVOY00000000.1 (B. xylanisolvens 18002P, F contorta 548 and 588 are de novo assemblies)
Supplementary_files_format_and_content: xslx files include DEseq2 values for each sample
|
| |
|
| Submission date |
Apr 26, 2020 |
| Last update date |
Sep 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) |
| GSE149357 |
RNA-seq of human gut bacterial isolates grown on seaweed polysaccharides |
|
| Relations |
| BioSample |
SAMN14732726 |
| SRA |
SRX8177514 |
