|
| Status |
Public on Mar 25, 2017 |
| Title |
RNA140717RH_4 |
| Sample type |
SRA |
| |
|
| Source name |
Dissected Tissue (Brain) - Striatum
|
| Organism |
Mus musculus |
| Characteristics |
group: HDID1 (selected line)
Sex: Female
|
| Treatment protocol |
Animals underwent the standard 4-day DID trial with three 2 hour exposures to a single bottle of 20% ethanol and a final day of 4 hour exposure. The DID trial always began 3 hours into the dark phase. BECs were obtained at the end of the 4th hour. A subgroup (N=20) of the animals were retested 3 weeks later. The remaining animals, 18 males and 17 females were sacrificed 3 weeks later and used for gene expression analyses. All animals were sacrificed between 10 AM and 2 PM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen brains were slightly thawed and dissected by hand under RNAse-free conditions. Using the optic chiasm as the rostral marker, a 2 mm coronal slice of brain tissue was isolated. Beginning at the medial ventral aspect of the striatum and recognizing that the striatum has a partial cone shape, the dissection moved dorsal 1 mm, followed by a cut to the lateral boundary of the striatum, with a final cut following the lateral-ventral boundary. The isolated tissue was immediately placed into 1 ml of Trizol (Invitrogen, Carlsbad, CA).
Library formation (polyA+, stranded) and sequencing were all performed according to Illumina’s specifications at the OHSU Massively Parallel Sequencing Shared Resource. Libraries were multiplexed 6 per lane, yielding approximately 25 to 30 million total reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
S4
|
| Data processing |
Base Calling was done through Illumina CASAVA software
FASTQC was run for data inspection
Alignment: Sequence data were then aligned using STAR (Spliced Transcripts Alignment to a Reference [Dobin et al. 2013]) allowing for a maximum of three mismatches per 100bp read. For all samples > 85% of the reads uniquely aligned.outFilterMismatchNmax=3,outFilterScoreMinOverLread=0.33,outFilterMismatchNoverLmax=0.03, outFilterMultimapNmax=1.
Reads Count: Using the Bedtools suite, reads were aligned to known genomic features to generate counts at the gene level.
Normalization: Gene expression data were imported into the R application environment; upper-quartile normalization was performed using the edgeR Bioconductor package (Robinson et al. 2010). The read density threshold for inclusion in the data analyses for genes was 30 or approximately 1 count per million reads.
Genome_build: Mus musculus (mm10)
Supplementary_files_format_and_content: RNA140717RH_mm10_exon_coverage_for_GEO.xlsx: Provides the phenotype related to each sample as well as the normalized (upper quartile) read counts for each gene for each sample
Supplementary_files_format_and_content: RNA140717RH_mm10_gene_coverage_for_GEO.xlsx: Provides the phenotype related to each sample as well as the normalized (upper quartile) read counts for each gene for each sample
|
| |
|
| Submission date |
Mar 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Priscila Darakjian |
| E-mail(s) |
darakjia@ohsu.edu
|
| Organization name |
Oregon Health and Science University
|
| Department |
Behavioral Neuroscience
|
| Street address |
3181 SW Sam Jackson Park Road, L470
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE97032 |
Alignment of the Transcriptome with Individual Variation in Animals Selectively Bred for High Drinking-In-the-Dark (HDID). |
|
| Relations |
| BioSample |
SAMN06642793 |
| SRA |
SRX2671714 |
