|
| Status |
Public on Jul 30, 2012 |
| Title |
Input DNA |
| Sample type |
SRA |
| |
|
| Source name |
G1ME cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: J1
cell type: G1ME
cell line: GATA1-deficient cell line with megakaryocyte and erythrocyte differentiation potential
protocol: Cells grown in TPO supernatant (10% v/v)
retrovirus: MigR1-HA-Gata1
fraction: input
|
| Treatment protocol |
Retroviral supernatant was added to the cells at 1e6 cells per ml, and the culture was centrifuged at 3200rpm for 90min. The cells were incuabted in the virus for an additional 4h, and then the virus was removed. The cells were crosslinked 48h later.
|
| Growth protocol |
G1ME cells were cultured in 1% TPO supernatant (v/v)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Isolated chromatin was sonicated and pre-cleared with isotype-matched mouse non-specific IgG. Chromatin immunprecipitation was carried out with a HA-tag antibody (Santa Crruz Biotechnology, sc-7392). The formaldehyde crosslinks were reversed by heating to 65-degrees overnight. RNA and protein were removed by treatment with RNAse A and Proteinase K, respectively, and the DNA was isolated using the Qiagen PCR Purification Kit. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# IP-102-1001).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Mappable reads were aligned to mouse genome mm9 using the Illumina pipeline
Peaks were identified with MACS v1.3.7.1 (Zhang Y, 2008) using the full set of unique IP tags as the ‘treatment’ and an equally-sized, randomly sampled subset of unique input tags as the ‘control,’ with the default p-value (10-5), and an ‘mfold’ value of 15. MACS was run three times for each IP tag set, using a different random subset of input, and the base-wise intersection of the three runs was obtained using intersectBed from BEDTools (Quinlan and Hall, 2010).
Genome Build:
TMC-INPUT-G1ME.bed: mm9
|
| |
|
| Submission date |
Feb 09, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Timothy Michael Chlon |
| E-mail(s) |
tchlon@u.northwestern.edu, timothy.chlon@cchmc.org, tchlon@gmail.com
|
| Organization name |
Cincinnati Children's
|
| Department |
Oncology
|
| Lab |
Wells
|
| Street address |
3333 Burnet Ave
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE35644 |
Genome-wide analysis of the role of FOG-1 in GATA-1 chromatin occupancy |
| GSE35708 |
Cofactor-mediated Restriction of GATA-1 Chromatin Occupancy Coordinates Lineage-specific Gene Expression |
|
| Relations |
| SRA |
SRX119326 |
| BioSample |
SAMN00783984 |
