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Sample GSM3244397 Query DataSets for GSM3244397
Status Public on Jun 01, 2020
Title Sample_16_48 hour post PHx 3
Sample type SRA
 
Source name 48 hour post PHx
Organism Mus musculus
Characteristics strain background: C3H/HeN
age: 8-10 weeks
fed state: Ad libitum
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”
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description phx_48hr_III_TCCGGAGA-ACGTCCTG
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 SAMN09601971
SRA SRX4341302

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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