|
| Status |
Public on Jun 01, 2020 |
| Title |
Sample_18_Wild Type + Chow 2 |
| Sample type |
SRA |
| |
|
| Source name |
Wild Type + Chow
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6J
genotype/variation: wild type
age: 16 weeks
fed state: 10 Hour Fast
tissue/cell type: Hepatocytes
|
| Growth protocol |
Organisms were housed in flow cages, following the standard 12 hour light/dark cycle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole livers or hepatocytes were isolated, flash frozen on Liquid nitrogen, and RNA was harvested using RNeasy tissue mini-kit (Qiagen, Cat No./ID: 74104)
RNA libraries were prepared for sequencing using standard Illumina protocols for “TruSeq Stranded mRNAseq Sample Prep kit”
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
C57_NC_Rep_II_ACTGATAT
|
| Data processing |
Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Adaptors were trimmed from the reads using trimmomatic
Reads were mapped to the genome using STAR_2.4.2a
Insert distribution calculated with Picard_1.119
Gene read_count values were calculated using htseq-counts along with the GRCm38 vM9 annotation file (.gff3).
Genome_build: GRCm38 vM9 mm10 (mus musculus)
Supplementary_files_format_and_content: consists of read_count values calculated for all genes annotated in vM10 for all samples submitted
|
| |
|
| Submission date |
Jul 04, 2018 |
| Last update date |
Jun 01, 2020 |
| Contact name |
Waqar Arif |
| E-mail(s) |
warif2@illinois.edu
|
| Organization name |
UIUC
|
| Department |
Biochemistry
|
| Lab |
461 Medical School Building
|
| Street address |
506 S. Mathews Avenue
|
| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE116627 |
High-throughput sequencing reveals induction of drug metabolism in various cholestatic livers |
|
| Relations |
| BioSample |
SAMN09601969 |
| SRA |
SRX4341304 |
