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Sample GSM4471971 Query DataSets for GSM4471971
Status Public on Jun 01, 2020
Title NULL_1F
Sample type SRA
Source name liver
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: Cyp2b-null
Sex: Female
Treatment protocol Cyp2b-null and hCYP2B6-Tg mice were fed a high-fat diet (60% fat) for 16 weeks.
Extracted molecule total RNA
Extraction protocol Livers were removed and stored at -80 degrees C. RNA was extracted from each treatment group (n=4) using Trizol.
Libraries were prepared using NEB Next Ultra RNA Library Prep kit.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description Rawcounts_CYP2B6_HFD_study.txt
Data processing Illumina Control Software/Real-Time Analysis (RTA) was used for base-calling.
Samples were sequenced to an average sequencing depth of 20,000,000 read pairs with a 2 x 150 paired-end module.
Quality metrics were checked using FastQC on all samples sequenced, and Trimmomatic was used to trim low quality bases.
Trimmed reads were aligned to the Mus musculus reference genome (GCF_000001635.25_GRCm38.p6) using GSNAP. Subread feature counts software finds reads that aligned with known genes.
Raw read counts and EdgeR were used to determine differential gene expression.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-deliminated text file includes raw counts for each sample.
Submission date Apr 10, 2020
Last update date Jun 01, 2020
Contact name William S Baldwin
Phone 915-491-7366
Organization name Clemson University
Department Biological Sciences
Lab Dr. William Baldwin
Street address 230 Parkway Dr
City Clemson
State/province South Carolina
ZIP/Postal code 29634
Country USA
Platform ID GPL24247
Series (1)
GSE148460 Role of human CYP2B6 in vivo in diet-induced obesity
BioSample SAMN14573717
SRA SRX8094496

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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