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Sample GSM1273201 Query DataSets for GSM1273201
Status Public on Jul 24, 2014
Title MYB prom donor A
Sample type SRA
 
Source name human erythroid progenitor (HEP)
Organism Homo sapiens
Characteristics cell type: human erythroid progenitor (HEP)
treatment: MYB promoter
Growth protocol Erythroid cells were cultured using a 2-phase liquid system. Mononuclear cells were isolated from peripheral blood by centrifugation on a gradient of Ficoll-Hypaque and cultured for 7 days in phase I medium which consists of serum-free StemSpan (Stem Cell Technologies) supplemented with 1 µg/mL cyclosporin A, 25 ng/mL interleukin-3, 50 ng/mL human stem cell factor (Sigma), and 0.01% bovine serum albumin. Cells were incubated at 37°C, 5% CO2. After 7 days, nonadherent cells were collected and reseeded at a concentration of 2.5 x 105 cells/mL in phase II medium (StemSpan supplemented with 10-7 M dexamethasone σ, 50 ng/mL stem cell factor, and 2 U/mL human recombinant erythropoietin [EPO; Sigma]). The cultures were diluted once or twice to maintain the cell concentration lower than 1 x 106 cells/mL in phase II. Cell samples were collected from phase II cultures on days 0, 2, 3, 4, 5, 6, and 7 and evaluated for number and viability.
Extracted molecule genomic DNA
Extraction protocol Cells were harvested at day 7-8 of culture and crosslinked using formaldehyde (1% final volume for ChIP-Seq, 2% final volume for 3C-Seq) and nuclei were isolated. For ChIP-Seq, nuclei were sonicated and protein-DNA complexes isolated using antibodies. For 3C-Seq, nuclei were digested and ligated under dilute conditions with primary and secondary restriction enzymes.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols. 3C-seq library preparation was described in detail in Stadhouders et al. Nature Protocols (2013).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina Genome Analyzer
 
Description 3C-Seq
Data processing Basecalls performed using CASAVA version 1.6 (Bustard)
Alignment performed using Bowtie against hg18 reference genome
Only unique mapping reads were used for the ChIP-seq downstream analysis
Genome_build: hg18
Supplementary_files_format_and_content: BigWig
 
Submission date Nov 21, 2013
Last update date May 15, 2019
Contact name Supat Thongjuea
E-mail(s) supat.thongjuea@ndcls.ox.ac.uk
Organization name The Weatherall Institute of Molecular Medicine
Department MRC Molecular Haematology Unit
Street address Headington
City Oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
 
Platform ID GPL9052
Series (1)
GSE52637 HBS1L-MYB intergenic variants modulate fetal hemoglobin via long-range MYB enhancers
Relations
BioSample SAMN02419109
SRA SRX381547

Supplementary file Size Download File type/resource
GSM1273201_HMP-HEP6.bw 178.6 Kb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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