|
| Status |
Public on Jun 29, 2013 |
| Title |
EXP_12_NoDp4 |
| Sample type |
SRA |
| |
|
| Source name |
Fecal
|
| Organisms |
[Clostridium] symbiosum; Bacteroides thetaiotaomicron VPI-5482; Bacteroides ovatus ATCC 8483; Bacteroides caccae ATCC 43185; Collinsella aerofaciens ATCC 25986; Marvinbryantia formatexigens DSM 14469; Escherichia coli str. K-12 substr. MG1655; Agathobacter rectalis ATCC 33656; Desulfovibrio piger GOR1 |
| Characteristics |
rna subtype: rRNA depleted total RNA
source: Fecal pellet from a mouse (NMRI) colonized with 8-gut bacteria. Mouse was fed a high fat/high sugar diet supplemented with 3% chondroitin sulfate (HF/HS+3%CS) TD.110459
processed data filename: EXP_12_NoDp4.counts.txt.gz
|
| Treatment protocol |
Fecal samples obtained from mice were immediately frozen at -80C and maintained at this temperature prior to processing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Each frozen sample was suspended in a solution containing 500 mL of acid-washed glass beads (Sigma-Aldrich), 500 mL of extraction buffer A (200 mM NaCl, 20 mM EDTA), 210 mL of 20% SDS, and 500 mL of a mixture of phenol:chloroform:isoamyl alcohol (125:24:1, pH 4.5; Ambion), and then lysed by using a bead beater (BioSpec Products; maximal setting; 4 min at room temperature). Cellular debris was removed by centrifugation (8,000 × g; 3 min at 4°C). The extraction was repeated, and nucleic acids were precipitated with isopropanol and sodium acetate (pH 5.5).
DNA libraries were prepared for sequencing using a modified version of Illumina's sample preparation protocol (see PMID:22030749 for protocol details)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Fecal pellet from a mouse (NMRI) colonized with 8-gut bacteria. Mouse was fed a high fat/high sugar diet supplemented with 3% chondroitin sulfate (HF/HS+3%CS) TD.110459
|
| Data processing |
Splitting barcodes - Sequence runs were split into their respective experiments using the 4-bp/8bp barcode at the beginning of each sequencing read.
Mapping reads - After dividing sequence runs by barcode, we mapped the reads to the relevant genomes using the ssaha2 algorithm
Handling ties - Reads that map non-uniquely were added to each gene in proportion to each gene’s fraction of unique-match counts (e.g., a non-unique read that maps equally well to gene A with 18 unique reads and gene B with 2 unique reads will be scored as 0.9 count to gene A and 0.1 count to gene B). We added a pseudocount (i.e. added 1) to each gene count prior to normalization to account for differences in sampling depth.
|
| |
|
| Submission date |
Jun 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Federico E Rey |
| E-mail(s) |
reyf@wustl.edu
|
| Phone |
314-963-0284
|
| Organization name |
Washington University
|
| Department |
Pathology
|
| Lab |
Gordon
|
| Street address |
4444 Forest Park Blvd
|
| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63108 |
| Country |
USA |
| |
|
| Platform ID |
GPL17383 |
| Series (2) |
| GSE48409 |
The metabolic niche of a prominent sulfate-reducing human gut bacterium [1] |
| GSE48809 |
The metabolic niche of a prominent sulfate-reducing human gut bacterium |
|
| Relations |
| SRA |
SRX316641 |
| BioSample |
SAMN02216928 |
