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Sample GSM2231951 Query DataSets for GSM2231951
Status Public on Nov 20, 2016
Title CB-24_L002_F4
Sample type SRA
 
Source name N/N_female_Striatum
Organism Mus musculus
Characteristics strain background: C57BL/6NJ
strain: Cyfip2N/N
genotype/variation: N/N; binge-prone
age: 82-84 days old
Sex: female
tissue: Striatum
cage: 425964
sampleID: CB-24
lane: L002_F4
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 two different lanes on 3 different days (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 R-subread (a R package). FeatureCounts was computed from R-subread. Count normalization was carried out with voom normalization using edgeR (v3.8.6) R package. Lane effect was adjusted by adding lane as a covariant. The gene are identified as entrezgene ensembl. 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 R-subread
 
Submission date Jul 12, 2016
Last update date May 15, 2019
Contact name Camron Bryant
E-mail(s) camron@bu.edu
Organization name Boston University School of Medicine
Department Pharmacology and Experimental Therapeutics
Lab Laboratory of Addiction Genetics
Street address 72 E. Concord St. R-604
City Boston
State/province Massachusetts (MA)
ZIP/Postal code 02118
Country USA
 
Platform ID GPL21103
Series (1)
GSE84329 RNA sequencing of Cyfip2N/- and Cyfip2N/N mice
Relations
BioSample SAMN05383014
SRA SRX1939564

Supplementary file Size Download File type/resource
GSM2231951_CB-24_L002_F4.featureCounts.txt.gz 116.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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