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Status |
Public on Mar 05, 2012 |
Title |
G1ME_INPUT (GAII) |
Sample type |
SRA |
|
|
Source name |
Megakaryocyte Progenitor Cell Line (G1ME)
|
Organism |
Mus musculus |
Characteristics |
cell line: G1ME Stage: Progenitor, GATA1-null antibody: none
|
Treatment protocol |
GATA1 ChIPs are from G1ME cells 48 hours after transduction with GATA1 retrovirus. All other ChIPs are from proliferating, untreated G1ME cells.
|
Growth protocol |
Cells were grown in alpha-MEM with 20% serum, 1% pen/strep and 1% TPO-conditioned medium, as described [Stachura et al., Blood 2006].
|
Extracted molecule |
genomic DNA |
Extraction protocol |
G1ME cells were crosslinked in 1% formaldehyde at room temperature and the crosslinking reaction was quenched with 125mM glycine. Cells were then lysed and isolated nuclei were lysed and sonicated to shear the chromatin. After centrifugation to remove debris, chromatin was pre-cleared with pre-immune IgG and protein G agarose beads. Pre-cleared chromatin was immunoprecipitated overnight, then RNase and proteinase treated, followed by organic extraction. Purified immunoprecipitated chromatin was subjected to end repair, dA addition, and linker ligation followed by 25 rounds of PCR amplification, gel purification, and an additional 15 rounds of PCR amplification and purification. Purified, amplified DNA was subjected to NanoDrop analysis and loaded on the flow cell of an Illumina GAII or GAIIx.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer II |
|
|
Description |
Input DNA Cells were derived from J1 ES cells [Fujiwara, PNAS, 1996; Stachura, Blood, 2006].
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Data processing |
Eland or eland_extended output from Illumina Pipeline was converted to BED format and analyzed with either MACS v1.3.7.1 (for transcription factors) using default p-value and mfold of 10 (ETS1), 15 (GATA1), or 32 (GATA2) or SICER (for histone marks) using default parameters. Datasets were analyzed 3 times against randomly selected size-matched subsets of a large INPUT dataset; the results of these analyses are the BED files labeled A, B, and C. The intersection of these 3 peak calls (BED files labeled ABC) were used for further analysis.
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|
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Submission date |
Aug 11, 2011 |
Last update date |
May 15, 2019 |
Contact name |
Louis C Dore |
E-mail(s) |
l-dore@northwestern.edu
|
Organization name |
Northwestern University
|
Department |
Feinberg School of Medicine
|
Lab |
Division of Hematology/Oncology
|
Street address |
303 E Superior St., Lurie Bldg 5-250D
|
City |
Chicago |
State/province |
IL |
ZIP/Postal code |
60611 |
Country |
USA |
|
|
Platform ID |
GPL9250 |
Series (1) |
GSE31331 |
Genome-wide transcription factor binding and chromatin methylation marks in the G1ME megakaryocytic progenitor model cell line |
|
Relations |
SRA |
SRX092602 |
BioSample |
SAMN00710550 |