|
| Status |
Public on Apr 01, 2014 |
| Title |
Input DNA |
| Sample type |
SRA |
| |
|
| Source name |
ChIP Input DNA
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse erythroleukemia cells
|
| Treatment protocol |
Cells were fixed in 1% formaldehyde for 5 min at room temperature.
|
| Growth protocol |
MEL cells were maintained in DMEM supplemented with 10% FCS at 37oC incubator.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
3-9 ng ChIP DNA was used in the direct polyA tailing step according to Helicos HeliScope standard procedure.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Helicos HeliScope |
| |
|
| Description |
Inupt data
We used streptavidin-based ChIP and ChIP-seq. No antibody was used. The product information for Dynabeads MyOne Streptavidin T1 (Invitrogen, Cat.# 656.01, lot # 757581130).
|
| Data processing |
Aligment: Sequence reads were obtained and mapped the mouse genome assembly mm9 (NCBI version 37) using Helisphere software with default parameters. Only the reads that were uniquely aligned to reference genome with read alignment score higher than 4.5 were retained for further analysis.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
|
| |
|
| Submission date |
Apr 02, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Xu |
| E-mail(s) |
Jian.Xu@stjude.org
|
| Phone |
9015955208
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Pathology
|
| Street address |
262 Danny Thomas Place, MS 345
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL14759 |
| Series (2) |
| GSE28334 |
BCL11A cistrome in mouse erythroleukemia (MEL) cells |
| GSE28355 |
Inactivation of BCL11A reactivates silenced human HbF in adult mice |
|
| Relations |
| SRA |
SRX131969 |
| BioSample |
SAMN00845030 |
