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Sample GSM3832660 Query DataSets for GSM3832660
Status Public on Dec 31, 2020
Title PB_CD34_D7_H3K27me3_R1 (ChIP-seq)
Sample type SRA
 
Source name PB_CD34_Bulk_Erytrhoid Day7
Organism Homo sapiens
Characteristics cell type: primary CD34+ HSPCs
passage: 20~30
chip antibody: H3K27me3(Cell Signaling Technology, CST#9733)
Growth protocol Cells were expanded in StemSpan serum-free expansion medium (SFEM; Stem Cell Technologies) supplemented with 1 µM dexamethasone, 1 µg/mL doxycycline, 50 ng/mL human stem cell factor (SCF), 3 units/mL erythropoietin (EPO), and 1% penicillin–streptomycin.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Data processing Basecalls performed using CASAVA
BWA (default parameter) was used to align reads to human genome hg19. Duplicated reads were marked by Picard, and uniquely mapped reads were retained by samtools (parameter “-q 1 -F 1024”).
We confirmed quality control results were good following the ENCODE guideline for CHIPSEQ, reads were then extend to the estimated fragment size(by SPP) and converted to bigwig files. We observed clear peaks observed by inspection on Integrated Genomics Viewer (Broad Institute) and there was high consistency among replicates.
Free pipeline to run with DNAnexus available at https://www.stjude.cloud/tools.html. Source code of ChIP-Seq pipeline to deposit on DNAnexus were also available at https://github.com/stjude/ChIP-Seq
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
 
Submission date May 30, 2019
Last update date Jan 01, 2021
Contact name Mitch Weiss
E-mail(s) mitch.weiss@stjude.org
Phone 9015953760
Organization name st jude children's research hospital
Department Hematology
Street address 262 Danny Thomas Place
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
 
Platform ID GPL20301
Series (1)
GSE115357 FBXO11-Mediated Proteolysis of BAHD1 Relieves PRC2-dependent Transcriptional Repression in Erythropoiesis
Relations
BioSample SAMN11891715
SRA SRX5931557

Supplementary file Size Download File type/resource
GSM3832660_PB_CD34_D7_H3K27me3_R1.bw 514.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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