|
| Status |
Public on Apr 10, 2016 |
| Title |
Drug_b2_33_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
C57BL/6J, striatum, RNAseq
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
treatment: Drug
tissue: striatum
batch: 2
rna integrity number: 8.75
|
| Treatment protocol |
All animals were bred at UNC from mice that were less than six generations removed from founders acquired from the Jackson Laboratory (Bar Harbor, ME).
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from striatum using Total RNA Purification 96-well Kit
Barcode libraries were created using Illumina TruSeq RNA sample preparation Kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
strand-specific
|
| Data processing |
We mapped lane-level reads to mm9 using Tophat v2.0.6 using default parameters and --library-type fr-firststrand option for strand-specific libraries
We removed reads with low quality score, potential PCR duplicates
The aligned lane-levl bam files were merged into one bam file for each sample
Mapped reads were summarized into gene-level expression estimates using Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: GTF files include RPKM values for each Sample generated from Cufflinks
|
| |
|
| Submission date |
Apr 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yunjung Kim |
| E-mail(s) |
ykim0224@gmail.com
|
| Organization name |
UNC at Chapel Hill
|
| Street address |
120 Mason farm road
|
| City |
chapel hill |
| State/province |
North Carolina |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE67750 |
Chronic haloperidol effects on gene expression in mouse [RNA-seq] |
| GSE67755 |
Chronic haloperidol effects on gene expression and chromatin accessibility in mouse brain |
|
| Relations |
| BioSample |
SAMN03470499 |
| SRA |
SRX986509 |
