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Sample GSM746565 Query DataSets for GSM746565
Status Public on Jul 05, 2011
Title H3K9me3_G1E_ChIPSeq_rep1
Sample type SRA
Source name G1E cells
Organism Mus musculus
Characteristics strain: 129
genotype/variation: Gata1-null
developmental stage/cell type: Erythroid committed, immature progenitor murine cell line
chip antibody target: H3K9me3
chip_antibody_provider: Abcam
chip_antibody_catalog: ab8898
chip_antibody_lot: unknown
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 HiSeq 2000
Description Chromatin IP against H3K9me3
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 GPL13112
Series (1)
GSE30142 Genome-wide maps of epigenetic features in G1E model and in mouse primary erythroblasts.
SRA SRX079871
BioSample SAMN00630471

Supplementary file Size Download File type/resource
GSM746565_h3k9m3_g1e_r1_mapped.txt.gz 2.4 Gb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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