|
| Status |
Public on Nov 09, 2016 |
| Title |
REST_antibody2_TAP_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
HCN cells in TAP or proliferative growth condition
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: hippocampal neural stem (HCN) cells derived from the adult rat brain
passages: multiple
growth condition: TAP
chip antibody: anti-REST (Hsieh lab homemade antibody)
|
| Growth protocol |
HCN cells were grown in quiescence (FGF2+BMP4+) or proliferation (FGF+ only) conditions on adherent plates as monolayer (typically 2–3 × 106 cells per 10cm plate) in DMEM:F12 (Omega Scientific Inc.) media supplemented with N2, glutamate and PSF.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Covaris ChIP protocol was followed https://ethanomics.files.wordpress.com/2012/01/chip_covaris4.pdf
Libraries were prepared according to Illumina's instructions and sequenced on Illumina platform, Illumina HiSeq 2500
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
REST_antibody1antibody2_TAP_ChIPSeq_HomerPk.txt
|
| Data processing |
ChIP-seq reads were aligned to the rn4 genome assembly using Bowtie2 with default settings
Data were filtered using the following specifications…
HOMER peak calling and merge peak function was used for peak calling, using default settings
Genome_build: rn4 (RGSC_v3.4)
Supplementary_files_format_and_content: Output from HOMER peak calling and merge peak function is shown
|
| |
|
| Submission date |
Jul 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jenny Hsieh |
| E-mail(s) |
[email protected]
|
| Phone |
12146456262
|
| Organization name |
UT Southwestern Medical Center
|
| Street address |
6001 Forest Park Road, NA6.514AA
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (2) |
| GSE70695 |
Genome-wide sequencing of REST binding (ChIP-seq) in adult hippocampal neural stem cells in vitro a.k.a. HCN cells in quiescent (iQNP) and proliferative (TAP) conditions |
| GSE70698 |
REST regulation of gene networks in adult neural stem cells |
|
| Relations |
| BioSample |
SAMN03853278 |
| SRA |
SRX1091090 |
