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Sample GSM3756128 Query DataSets for GSM3756128
Status Public on Oct 27, 2021
Title Male_CAST_PolyA_RNA_Repl3_G164_M13
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics strain: C57BL/6J (Jackson Labs, cat#:000664)
rna isolation: 1 microgram total liver RNA
Sex: Male
age: 8 weeks
Growth protocol Male and female C57BL/6J and CAST/EiJ mice, 8-9 weeks of age, were purchased from Jackson Labs.
Extracted molecule polyA RNA
Extraction protocol Snap frozen liver was used as input for RNA purification using TRIzol reagent (Invitrogen, cat#:15596026) following the manufacturer’s directions. Total RNA was quantified using the Qubit RNA BR kit (Invitrogen, cat#:Q10210). 1 microgram of total RNA per sample was used as input for library preparation.
Samples were prepared for sequencing with NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB, cat#:E7420) with the PolyA selection with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, cat#:E7490).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description RNA-seq Library
Data processing READ MAPPING: Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotech, 2010)
QUANTIFICATION: FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq and long noncoding genes (Lodato et al 2017). Transcripts were quantified by counting sequence reads that map to a the gene body of a gene.
DIFFERENTIAL EXPRESSION: Quantification of differential expression was performed using edgeR (Robinson, 2010, Bioinformatics)
Genome_build: mm9
Supplementary_files_format_and_content: EdgeR output for CAST and B6 strains, and FPKM normalized read counts for protein coding and noncoding genes (FPKM_perGene.txt), where BM indicates livers of five individual C57BL/6J males, BF indicates C57BL/6J females, CM indicates livers of five individual CAST/EiJ males, CF indicates CAST/EiJ females.
 
Submission date May 08, 2019
Last update date Oct 27, 2021
Contact name David J. Waxman
E-mail(s) djw@bu.edu
Organization name Boston University
Department Department of Biology and Bioinformatics Program
Street address 5 Cummington Mall
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL24247
Series (2)
GSE130913 RNA-seq in male and female mouse liver for two mouse strains: C57BL/6J and CAST/EiJ.
GSE130914 Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model
Relations
BioSample SAMN11607984
SRA SRX5809893

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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