NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2227578 Query DataSets for GSM2227578
Status Public on Dec 01, 2023
Title CD34_CHD7_Input
Sample type SRA
 
Source name CD34+ cells
Organism Homo sapiens
Characteristics tissue: mobilized peripheral blood
cell type: CD34 positive cells
antibody: None
Treatment protocol None.
Growth protocol Human mobilized peripheral CD34+ cells were thawed and grown in StemSpan SFEM media supplemented with 2% pen/strep and 1% StemSpan CC100 cocktail (Stem Cell Technologies) for 5 days. Cells were fixed and collected on day 5 for ChIP-seq.
Extracted molecule genomic DNA
Extraction protocol CD34+ cells were fixed in 1% formaldehyde for 10 minutes and lysed to collect nuclei for sonication, followed by ChIP with antibody.
Library synthesis was performed using TruSeq ChIP Library Prep Kit (Illumina).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Ordered from Fred Hutchinson Cancer Research Center
Data processing Reads were aligned to human reference genome hg19 using Bowtie Version 0.12.9 with parameters -n 2 -S -k 2 -m 2 -best
Regions enriched for CHD7 were identified using SICER with parameters -w 200 -I 200 -g 400 -e 1e1
Regions enriched for histone H3K27ac were identified using MACS with input control and parameters -p 1e-9 -keep-dup=auto
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Alignment and bed files of binding peaks
 
Submission date Jul 07, 2016
Last update date Dec 01, 2023
Contact name Leonard Zon
E-mail(s) zon@enders.tch.harvard.edu
Organization name Boston Children's Hospital
Department Oncology/Hematology
Street address 1 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL11154
Series (2)
GSE84130 CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation [CD34 ChIP-seq]
GSE84131 CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation
Relations
BioSample SAMN05363828
SRA SRX1901614

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap