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| Status |
Public on Nov 26, 2016 |
| Title |
RNA sequencing of C57BL/6NJ (B6NJ) x C57BL/6J (B6J) - F2 mice |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
RNA-seq analysis of 16 B6J x B6NJ-F2 mice which are homozygous for either the wild-type B6J allele (binge-resistant; J/J) or mutant B6NJ allele (binge-prone; N/N), at rs240617401, a marker denoting a missense SNP in Cyfip2. Genotype identity is denoted as either J for binge-resistant; J/J, or N for binge-prone; N/N.
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| Overall design |
A sample size of N=8 per genotype was employed (4 females, 4 males; 69-100 days old at the time of sacrifice). 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). FASTQ files were quality checked via FASTQC and all samples exhibited Phred quality scores greater than 30 (i.e. less than 0.1% sequencing error). FASTQ files were used to align reads to the reference genome using TopHat (mm10; UCSC Genome Browser). Read counts per gene were quantified using the HTSeq Python package.
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| Contributor(s) |
Kirkpatrick S, Bryant C, Reed E |
| Citation(s) |
27914629 |
| |
| 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 |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (64)
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| Relations |
| BioProject |
PRJNA328473 |
| SRA |
SRP078250 |
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