|
| Status |
Public on Sep 01, 2014 |
| Title |
Control-microbiota recipient (CT3) |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
age: 8 weeks
gender: Female
strain: Germ-free Swiss Webster
treatment: conventionalized with control-microbiota
diet: D12451: 45% kCAL from fat
tissue: liver
|
| Treatment protocol |
Control mice did not receive antibiotics, LDP mice received low-dose penicillin from birth. Microbiota from control and LDP mice were used to then convetionalized germ-free swiss-webster mice, which did not receive further antibiotic treatment.
|
| Growth protocol |
C57BL6 mice were weaned at 4 weeks of age onto normal chow, then switched to a high fat diet (45% kcal from fat) at 6 weeks of age. Or germ-free swiss webster mice were conventionalized with control or LDP-microbiota at 3 weeks of age, and fed a high fat diet (45% kcal from fat). Livers were collected at 8 weeks of age
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini Kit (Qiagen, Valencia CA)
RNA-seq libraries were generated using the TruSeq v2 RNA sample prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file: CoxBlaser_NYGC_femaleSamples_count_matrix.txt
|
| Data processing |
Alignment to the genome build mm10 with STAR (Dobin et al. 2012) v.2.3.0e (female samples) and v.2.3.1x (male samples)
Quantification of the UCSC genes with HTSeq-count v0.5.3p9 (female samples) or featureCounts v1.4.3-p1 (male samples)
Differential expression analysis performed with DESeq (Bioconductor)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited .txt files report counts
|
| |
|
| Submission date |
May 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiho Sohn |
| E-mail(s) |
jihosohn@buffalo.edu
|
| Organization name |
SUNY Buffalo
|
| Department |
Oral Biology
|
| Lab |
Keith Kirkwood
|
| Street address |
3435 Main Street, 644 Biomedical Research Building
|
| City |
Buffalo |
| State/province |
New York |
| ZIP/Postal code |
14214 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE58087 |
Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences |
| GSE58089 |
Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN02803861 |
| SRA |
SRX555158 |
