|
| Status |
Public on Nov 20, 2016 |
| Title |
CB-29_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: 425966
sampleID: CB-29
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 -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 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) |
[email protected]
|
| 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 |
SAMN05383019 |
| SRA |
SRX1939569 |
