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Sample GSM3756133 Query DataSets for GSM3756133
Status Public on Oct 27, 2021
Title Female_CAST_PolyA_RNA_Repl3_G164_M18
Sample type SRA
Source name Liver
Organism Mus musculus
Characteristics strain: CAST/EiJ (Jackson Labs, cat#:000928)
rna isolation: 1 microgram total liver RNA
Sex: Female
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
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
BioSample SAMN11607979
SRA SRX5809898

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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