|
Status |
Public on Jun 01, 2020 |
Title |
Sample_22_fl/fl Fxr fl/fl Shp + Chow 2 |
Sample type |
SRA |
|
|
Source name |
fl/fl Fxr fl/fl Shp + Chow
|
Organism |
Mus musculus |
Characteristics |
strain background: C57BL/6J genotype/variation: fl/fl Fxr fl/fl Shp age: 10-12 weeks fed state: 8-10 hour fast tissue/cell type: Whole Liver
|
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”
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
Ctrl_Chow_II_ATTCAGAA-AGGCTATA
|
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
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|
|
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 |
SAMN09601965 |
SRA |
SRX4341308 |