NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5530945 Query DataSets for GSM5530945
Status Public on May 25, 2022
Title Fetal_H3K27ac_r1
Sample type SRA
 
Source name Fetal erythroblasts
Organism Homo sapiens
Characteristics tissue/cell type: CD34+ cells derived from fetal liver
cell type: Erythroid cells
differentiation: Differentiated day11
chip antibody: H3K27ac (Thermo, MA5-23516, lot VL3008252)
Growth protocol Human CD34+ HSPCs were cultured using a three-phase protocol. For phase 1 medium, IMDM was supplemented with 100 ng/mL of human stem cell factor, 1 ng/mL of interleukin-3, 3 units/mL of erythropoietin, 2% penicillin/streptomycin, 200 μg/mL of holotransferrin, 10 μg/mL of insulin, 5% human male A/B plasma, and 10 mg/mL of heparin. For phase 2 medium, the interleukin-3 was withdrawn after 9 days of culture. For phase 3, the cells were cultured with IMDM supplemented with 3 units/mL of erythropoietin, 2% penicillin/streptomycin, 1 mg/mL of holotransferrin, 10 μg/mL of insulin, 5% human A/B plasma, and 10 μg/mL of heparin.
Extracted molecule genomic DNA
Extraction protocol 500-800k cells were collected for CUT&RUN. CUT&RUN were performed using the CUT&RUN Assay Kit (Cell Signaling, #86652S) according to the manufacturer’s instructions.
Samples were processed for library construction for Illumina sequencing using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645S) according to NEB's instructions..
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model NextSeq 2000
 
Data processing library strategy: CUT&RUN
Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1
Reads were mapped to reference genome hg38 with Bowtie 1.3.0 using parameters --best --sam --chunkmbs 256 -X 800. Peaks were called using MACS2. Peaks overlapped with blacklist were further filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files with read coverage; bed files of peaks
 
Submission date Aug 21, 2021
Last update date May 27, 2022
Contact name Peng Huang
E-mail(s) waliays@gmail.com
Organization name Guangzhou Medical University
Department GMU-GIBH Joint School of Life Sciences
Lab Peng Huang
Street address Xinzao, Panyu District
City Guangzhou
State/province Guangdong
ZIP/Postal code 511436
Country China
 
Platform ID GPL30173
Series (2)
GSE173587 HIC2 represses BCL11A transcription to regulate hemoglobin switching during development
GSE182530 HIC2 represses BCL11A transcription to regulate hemoglobin switching during development [CUT&RUN]
Relations
BioSample SAMN20923620
SRA SRX11857116

Supplementary file Size Download File type/resource
GSM5530945_3434_hg38.bigwig 42.8 Mb (ftp)(http) BIGWIG
GSM5530945_3434_peaks_clean.bed.gz 799.4 Kb (ftp)(http) BED
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