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Sample GSM2230335 Query DataSets for GSM2230335
Status Public on Nov 26, 2016
Title Sample_CB-1_L001_2
Sample type SRA
 
Source name wild-type B6J allele_female_striatum
Organism Mus musculus
Characteristics strain background: C57BL/6NJ (B6NJ) x C57BL/6J (B6J)
genotype/variation: homozygous for wild-type B6J allele (binge-resistant; J/J)
age: 69-100 days old at the time of sacrifice
Sex: female
tissue: Striatum
sampleID: CB-1
lane: L001_2
cage #: 168320
Extracted molecule total RNA
Extraction protocol Striatum punches were harvested on Day 24 immediately following the 5-min behavioral test on the EPM, stored in RNAlater for 48 h, blotted dry with a kimwipe, and transferred to -80ÂșC.
Total RNA was isolated and shipped to the University of Chicago Genomics Core Facility for cDNA library preparation using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (50 bp single-end reads). Samples were sequenced using the Illumina HiSeq 4000 with 16 samples per lane over four lanes (technical quadruplicates).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Samples were run across four lanes on 4 different flow cells and 50bp reads for each sample were generated via the Illumina HiSeq 4000.
Fastq files are quality checked with FastQC (v0.11.3).
Single-end reads were mapped to the mouse genome (mm10) using tophat (v2.1.0). Per gene read counts were computed using HTSeq (v0.6.1p1). Count normalization was carried out with weighted trimmed mean of M-values (TMM) using edgeR (v3.8.6) R package. Differential gene expression was carried out using the Limma (v3.22.7) R package.
Genome_build: mm10
Supplementary_files_format_and_content: Tab Delimited file of read counts per gene from HTSeq
 
Submission date Jul 11, 2016
Last update date May 15, 2019
Contact name Eric R Reed
E-mail(s) eric.reed@tufts.edu
Organization name Tufts University
Department Data Intensive Studies Center
Street address 419 Boston Ave.
City Medford
State/province MA
ZIP/Postal code 02155
Country USA
 
Platform ID GPL21103
Series (1)
GSE84252 RNA sequencing of C57BL/6NJ (B6NJ) x C57BL/6J (B6J) - F2 mice
Relations
BioSample SAMN05372001
SRA SRX1925206

Supplementary file Size Download File type/resource
GSM2230335_Sample_CB-1_L001_2.txt.gz 96.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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