|
| Status |
Public on Apr 10, 2016 |
| Title |
drug_st2_DNase-seq |
| Sample type |
SRA |
| |
|
| Source name |
C57BL/6J, striatum, DNase-seq
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
treatment: drug
tissue: striatum
lane: 5
|
| 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 |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from mouse brain samples
The extracted nuclei were digested with different amounts of DNase I for 16 min at 37° C. The reactions were terminated by the addition of 50 mM EDTA. Libraries were constructed from pooled digests and sequenced.
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
read sequences were aligned to mm9 using bowtie with parameters (-m 1 --best --strata)
we filtered to remove quality score < 10, PCR duplicates.
We used F-seq for estimation of enriched peaks to identify potential open chromatin regions
Genome_build: mm9
Supplementary_files_format_and_content: bed files for DNase I cut peak regions
|
| |
|
| 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) |
| GSE67746 |
Chronic haloperidol effects on open chromatin accessibility in mouse [DNase-seq] |
| GSE67755 |
Chronic haloperidol effects on gene expression and chromatin accessibility in mouse brain |
|
| Relations |
| BioSample |
SAMN03470485 |
| SRA |
SRX986476 |
