|
| Status |
Public on Nov 26, 2016 |
| Title |
Sample_CB-3_L002_2 |
| Sample type |
SRA |
| |
|
| Source name |
wild-type B6J allele_male_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: male
tissue: Striatum
sampleID: CB-3
lane: L002_2
cage #: 167163
|
| 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 -80ºC.
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 |
SAMN05372010 |
| SRA |
SRX1925215 |
