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Sample GSM777094 Query DataSets for GSM777094
Status Public on Mar 05, 2012
Title G1ME_H3K4me3
Sample type SRA
Source name Megakaryocyte Progenitor Cell Line (G1ME)
Organism Mus musculus
Characteristics cell line: G1ME
Stage: Progenitor, GATA1-null
antibody: anti-H3K4me3
antibody catalog number: 07-473
antibody vendor: Millipore
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.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Chromatin IP against H3K4me3
Cells were derived from J1 ES cells [Fujiwara, PNAS, 1996; Stachura, Blood, 2006].
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.
Submission date Aug 11, 2011
Last update date May 15, 2019
Contact name Louis C Dore
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 GPL11002
Series (1)
GSE31331 Genome-wide transcription factor binding and chromatin methylation marks in the G1ME megakaryocytic progenitor model cell line
SRA SRX092600
BioSample SAMN00710548

Supplementary file Size Download File type/resource
GSM777094_H3K4me3.bed.gz 233.4 Mb (ftp)(http) BED
GSM777094_H3K4me3_ABC_peaks.bed.gz 239.7 Kb (ftp)(http) BED
GSM777094_H3K4me3_A_peaks.bed.gz 980.6 Kb (ftp)(http) BED
GSM777094_H3K4me3_B_peaks.bed.gz 980.6 Kb (ftp)(http) BED
GSM777094_H3K4me3_C_peaks.bed.gz 983.2 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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