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Sample GSM746575 Query DataSets for GSM746575
Status Public on Jul 05, 2011
Title H3K4me3_G1EER4_ChIPSeq_rep1
Sample type SRA
Source name G1E-ER4+E2 cells
Organism Mus musculus
Characteristics developmental stage/cell type: recapitulated erythroid differentiation after induction by estradiol treatment for 24hr.
Treatment protocol G1E-ER4 cells were induced in the presence of 10^(-8) mol/L (beta)-estradiol for 24 hours.
Growth protocol G1E and G1E-ER4 cells were grown in IMDM media with 15% fetal calf serum 2U/ml erythropoietin (Amgen’s EpoGen) and 50ng/ml stem cell factor. Erythroid cells were obtained by enriching fresh E14.5 fetal liver preps for Ter119-positive cells using an anti-Ter119 antibody coupled to magnetic beads (StemCell EasySep Kit #18554).
Extracted molecule genomic DNA
Extraction protocol For ChIP-seq, ChIP DNA or input DNA was amplified by Illumina ChIP-Seq library preparation kit. To prepare the sequencing libraries, the ChIP DNA fragments were repaired to generate blunt ends, with a single A nucleotide adding to each end. Double-stranded Illumina adaptors were ligated to both ends of the fragments. Ligation products were amplified by 18 cycles of PCR, and the PCR products between 200 and 400 bp were gel purified. The quality of the library was evaluated by qPCR and bio-analyzer to make sure it meets the requirements by Illumina.
For DNase-seq, nuclei isolated from G1E and G1E-ER4+E2 cells were lightly digested with DNaseI to expose regions hypersensitive to the enzyme. Digested ends of the DNA were ligated to a biotinylated and phosphorylated linker and enriched on streptavidin-coated DynaI beads. This was followed by MmeI restriction enzyme digestion, which cuts 20 bases downstream of the recognition site contained within the biotinylated linker. A second linker was ligated to the MmeI cut sites and ligation-mediated polymerase chain reaction performed prior to being sequenced.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Chromatin IP against H3K4me3
Data processing Alignment: Sequencing reads were mapped to the mouse genome (mm8 assembly) using the program Efficient Local Alignment of Nucleotide Data (ELAND) or Bowtie.
Submission date Jun 22, 2011
Last update date May 15, 2019
Contact name Ross Hardison
Organization name Pennsylvania State University
Street address 303 Wartik Lab
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
Platform ID GPL11002
Series (1)
GSE30142 Genome-wide maps of epigenetic features in G1E model and in mouse primary erythroblasts.
SRA SRX079881
BioSample SAMN00630481

Supplementary file Size Download File type/resource
GSM746575_h3k4m3_er4_r1_mapped.txt.gz 394.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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