|
| Status |
Public on Jul 12, 2013 |
| Title |
NoDp1 |
| Sample type |
SRA |
| |
|
| Source name |
Proximal colon from gnotobiotic mice colonized with defined bacterial assemblage
|
| Organism |
Mus musculus |
| Characteristics |
age: 7-8 weeks old
strain: NMRI
diet: High fat/ High sugar supplemented with 3% chondroitin sulfate
colonization: mice colonized with 8 human gut bacterial species
|
| Treatment protocol |
proximal colon samples obtained from mice were immediately frozen at -80C and maintained at this temperature prior to processing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Proximal colon samples were homogenized in trizol and purified using the Qiagen Rneasy kit including the in column DNAse treatment. mRNA was furter purified using Dynabeads mRNA purification kit (Invitrogen) following manufacters protocol
cDNA libraries were prepared for sequencing using a modified version of Illumina's sample preparation protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mice colonized with 8 human gut bacterial species
|
| Data processing |
Splitting barcodes - Sequence runs were split into their respective experiments using the 4-bp barcode at the beginning of each sequencing read.
Mapping reads - After trimming reads to 42nt and dividing sequence runs by barcode, we mapped the reads to the mouse genome using the TopHat and Bowtie algorithm
Counts were normalized to upper quartile and significance between groups was assessed using CyberT
Genome_build: genome mm37.63 (from ENSEMBL).
|
| |
|
| Submission date |
Jul 11, 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 |
GPL13112 |
| Series (2) |
| GSE48808 |
The metabolic niche of a prominent sulfate-reducing human gut bacterium [3] |
| GSE48809 |
The metabolic niche of a prominent sulfate-reducing human gut bacterium |
|
| Relations |
| BioSample |
SAMN02231415 |
| SRA |
SRX320405 |
