|
| Status |
Public on Jan 25, 2023 |
| Title |
abx_2-2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C56Bl/6j
antibiotics: yes
diet: AIN-76a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were removed, flash frozen in RNALater on dry ice, and RNA was harvested using Trizol Reagent followed by RNA cleanup using Qiagen Rneasy Mini Kit.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA HT Sample Prep Kit (Illumina) as per standard protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
9samp_counts_salmonTxi.csv
|
| Data processing |
Raw data was counted against transcripts described in gencode version M21 with salmon. Transcipt counts were summarized to gene-level with tximport in R.
Genome_build: GRCm38, gene models from gencode version M21
Supplementary_files_format_and_content: comma separated values, raw counts per gene, Ensembl gene IDs with version
|
| |
|
| Submission date |
Jan 27, 2020 |
| Last update date |
Jan 25, 2023 |
| Contact name |
Gary D Wu |
| Organization name |
University of Pennsylvania
|
| Department |
Department of Medicine, Division of Gastroenterology
|
| Street address |
915 Biomedical Research Building, 421 Curie Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE144266 |
Short Chain Fatty Acid Independent Hepatic Histone Acetylation Patterns, Induced by Microbiota Exposure, are Irreversible |
|
| Relations |
| BioSample |
SAMN13926806 |
| SRA |
SRX7634758 |
