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Sample GSM6616188 Query DataSets for GSM6616188
Status Public on May 06, 2023
Title HiChIP_GATA1_Day5_Rep1
Sample type SRA
 
Source name Cord Blood
Organism Homo sapiens
Characteristics tissue: Cord Blood
cell line: Erythroid progenitor (Day5)
cell type: Erythroid progenitor (Day5)
genotype: pooled
Extracted molecule genomic DNA
Extraction protocol For GATA1 HiChIP, ten million Day-5 erythroid progenitors / Day-12 erythroblasts generated from ex vivo CD34+ erythroid differentiation culture were used. In brief, after fixation with 1% formaldehyde, cells were digested for 2 hours at 37°C using 375U of MboI (NEB, Cat. #R0147). After biotin filling, proximity ligation was carried out with 4000U T4 DNA Ligase (NEB, Cat. # M0202M) for 2 hours at 25°C. Sonication of re-suspended nuclei was performed by Covaris M220 sonicator. Following an overnight incubation with anti-GATA1 antibody (abcam, Cat.# ab11852), 100 µL Protein A Magnetic Beads were added at 4°C and incubated for 2 hours. Bound DNA–protein complexes were eluted and reverse-crosslinked after a series of washes.
After reverse-crosslinking, ligation fragments containing biotin were immobilized on MyOne Streptavidin C1 beads (ThermoFisher Cat.#: 65602), and the library was prepared using the Tn5 transposome DNA library preparation kit (Vazyme, Cat.# TD502) as per the manufacturer’s protocol. DNA was then subjected to double-size selection using DNA Clean Beads (Vazyme, Cat. # N411) in order to isolate fragments between 300 and 600bp. Two biological replicates per condition were sequenced in a NovaSeq 6000 (S4, PE150, Illumina) by Novogene (Beijing).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing In brief, the raw reads of HiChIP library were mapped with hg19 and further filtered with HiC-Pro (version 3.10.0, https://github.com/nservant/HiC-Pro) to remove pairs with multiple hits, MAPQ <10, singleton, dangling end, self-circle, and PCR duplicates.
All biological replicates (HiChIP GATA1, generated in this paper) were processed individually to assess quality and then combined for downstream analyses and visualization (HiChIP of H3K27ac are obtained from public dataset without replicates). Correlation of replicates was calculated by Stratum-adjusted Correlation Coefficient (SCC) method with HiCRep (http://github.com/qunhualilab/hicrep) at 10 kb, 20 kb and 50 kb.
HiChIP datasets then were processed by FitHiChIP (https://github.com/ay-lab/FitHiChIP) after subset to the same valid interaction numbers. The following parameters were used to call HiChIP loops: 5,000 bp resolution, 10000-2000000 distance threshold, FDR 0.05, coverage specific bias correction, merged nearby peak to all interactions, L model for both H3K27ac and GATA1 HiChIP. To simplify the analysis, we designate H3K27ac/ GATA1 peaks in Ery-Pro/ Ery-Pre stage to represent Day5/12 H3K27ac/ GATA1 peaks respectively. GenomicInteractions (https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions) was used to designated P-P, E-P and E-E loops in respective stage.
Differential GATA1 HiChIP loops were identified via “DiffAnalysisHiChIP.r” script of FitHiChIP with parameters as follow: FDR < 0.01, FoldChangeThr > 2
Virtual 4C was performed as described before with minor modifications. In brief, the mates of reads that mapped at the viewpoints region at one side were extract, and visualization was done using average CPM signals per condition at 200 bp bin size and 2 kb window.
Assembly: hg19
Supplementary files format and content: mcool
Supplementary files format and content: loopfiles.tar.gz; compressed package containing WashU.bed.gz and .tbi
Library strategy: HiChIP
 
Submission date Oct 04, 2022
Last update date May 06, 2023
Contact name Dong Li
E-mail(s) lidongpaul@gmail.com
Organization name Peking University
Department College of Life Science
Lab Hsiang-Ying (Sherry) Lee
Street address No.5 Yiheyuan Road, Haidian District,
City Beijing
State/province Beijing
ZIP/Postal code 100871
Country China
 
Platform ID GPL24676
Series (2)
GSE214807 Stage-specific erythroid cell three-dimensional chromatin architecture and transcription factors binding provide insight of human erythropoiesis [HiChIP]
GSE214811 Stage-specific erythroid cell three-dimensional chromatin architecture and transcription factors binding provide insight of human erythropoiesis
Relations
BioSample SAMN30996488
SRA SRX17691796

Supplementary file Size Download File type/resource
GSM6616188_D5GATA1_HiChIP_rep1.mcool 567.3 Mb (ftp)(http) MCOOL
GSM6616188_D5GATA1_HiChIP_rep1_loopfiles.tar.gz 451.9 Kb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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