|
| Status |
Public on Oct 03, 2012 |
| Title |
Input_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Embyonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: 129SV embryonic stem cells
passages: 13-18
chip antibody: none
|
| Growth protocol |
Embryonic stem (R1ES) cells (passage 13-18) were routinely grown on gelatin coated tissue culture plates in complete growth medium in presence of LIF (1000 U/ml) as described in our previous publication (Nair 2006, Apoptosis 11: 955-966).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP assays were performed using EZ-ChIP kit (Cat#17-371) from Upstate Biotechnology (Millipore) according to the manufacturer's instructions. Briefly, 5 x107 cells were trypsinized, fixed with 1% formaldehyde, resuspended in lysis buffer, and fragmented with a Bioruptor UCD-200 Sonifier (Diagenode Inc. NY) to a size range of 200 to 1,000 bases. Solubilized chromatin was diluted 10-fold in ChIP dilution buffer and after removal of a control aliquot (Input), incubated at 4ºC overnight with antibody against LSD1 (Abcam #07-449) or dimethyl histone H3 Lys4 (Cell Signaling Technology #9753). Control IgG was used as a negative control in all ChIP experiments. Immune-complexes were purified using spin columns and libraries were prepared according to Illumina's instructions for preparing samples for ChIP sequencing of DNA (Part # 11257047). Approximately 200 bp DNA fragments were purified from the library after ressolving on an agarose gel. DNA was captured on an Illumina flow cell for cluster generation. Libraries were then subjected to sequencing in an Illumina Genome Analyzer II to generate 36 bp reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Genomic DNA used for ChIP
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the mouse mm9 genome (NCBI, Build 37) using the Illumina Genome Analyzer G2 Pipeline. All reads that is uniquely mapped to mm9 with two or fewer mismatches were retained. We kept only one read if multuple reads were mapped to the same position of mm9.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
|
| |
|
| Submission date |
Oct 09, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Venugopalan Nair |
| E-mail(s) |
venugopalan.nair@mssm.edu
|
| Phone |
212-241-5809
|
| Fax |
212-289-4107
|
| Organization name |
Mount Sinai School of Medicine
|
| Department |
Neurology
|
| Street address |
1 Gustave L. Levy Place
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE18515 |
Genome-wide map of lysine specific demethylase 1 (LSD1) in mouse embryonic stem cells. |
|
| Relations |
| SRA |
SRX019358 |
| BioSample |
SAMN00011729 |
