|
Status |
Public on Apr 10, 2016 |
Title |
placebo_b1_20_RNA-seq |
Sample type |
SRA |
|
|
Source name |
C57BL/6J, striatum, RNAseq
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6J treatment: placebo tissue: striatum batch: 1 rna integrity number: 7.77
|
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 |
SAMN03470509 |
SRA |
SRX986491 |