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Series GSE231422 Query DataSets for GSE231422
Status Public on Aug 21, 2023
Title Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC [ChIPmentation]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Hematopoietic stem and progenitor cells (HSPCs) rely on a complex interplay of transcription factors (TFs) to regulate their differentiation into mature blood cells. A heptad of TFs - FLI1, ERG, GATA2, RUNX1, TAL1, LYL1, LMO2 - has been shown to bind to regulatory elements in bulk CD34+ HSPCs. However, whether specific combinations of these TFs have distinct roles in regulating hematopoietic differentiation remained unknown. In this study, we mapped the genome-wide binding profiles of these TFs and other chromatin-associated markers in distinct HSPC subsets (HSC, CMP, GMP, MEP). We found that the heptad occupancy and enhancer-promoter interactions varied significantly across cell types and were associated with cell-type specific gene expression. Moreover, we observed distinct regulatory elements that were enriched with specific combinations of TFs, such as stem-cell specific elements with ERG, and myeloid and megakaryocyte-erythroid specific elements with combinations of FLI1, RUNX1, GATA2, TAL1, LYL1, and LMO2. These findings suggest that specific combinations of TFs play critical roles in the regulation of hematopoietic differentiation, and provide a valuable resource for the development of targeted therapies to manipulate specific HSPC subsets.
 
Overall design ChIPmentation
 
Contributor(s) Subramanian S, Thoms J, Pimanda J
Citation(s) 37595278
Submission date May 01, 2023
Last update date Aug 21, 2023
Contact name Julie Thoms
E-mail(s) j.thoms@unsw.edu.au
Organization name UNSW Sydney
Department Adult Cancer Program
Street address Level 2, C25 Lowy Cancer Research Centre, UNSW Sydney, High St
City Randwick
State/province NSW
ZIP/Postal code 2052
Country Australia
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (132)
GSM7277346 ChIPmentation_CMP_ERG_rep1
GSM7277347 ChIPmentation_CMP_ERG_rep2
GSM7277348 ChIPmentation_CMP_ERG_rep3
This SubSeries is part of SuperSeries:
GSE231486 Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC
Relations
BioProject PRJNA965795

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE231422_CTCF_CMP_peaks.narrowPeak.gz 1.0 Mb (ftp)(http) NARROWPEAK
GSE231422_CTCF_GMP_peaks.narrowPeak.gz 1.0 Mb (ftp)(http) NARROWPEAK
GSE231422_CTCF_HSC_peaks.narrowPeak.gz 689.2 Kb (ftp)(http) NARROWPEAK
GSE231422_CTCF_MEP_peaks.narrowPeak.gz 931.1 Kb (ftp)(http) NARROWPEAK
GSE231422_Coverage_CTCF_CMP_merge_clip.bw 207.0 Mb (ftp)(http) BW
GSE231422_Coverage_CTCF_GMP_merge_clip.bw 206.0 Mb (ftp)(http) BW
GSE231422_Coverage_CTCF_HSC.bw 174.3 Mb (ftp)(http) BW
GSE231422_Coverage_CTCF_MEP_merge_clip.bw 226.4 Mb (ftp)(http) BW
GSE231422_Coverage_ERG_CMP_merge_clip.bw 242.4 Mb (ftp)(http) BW
GSE231422_Coverage_ERG_GMP_merge_clip.bw 164.3 Mb (ftp)(http) BW
GSE231422_Coverage_ERG_HSC.bw 191.0 Mb (ftp)(http) BW
GSE231422_Coverage_ERG_MEP_merge_clip.bw 193.8 Mb (ftp)(http) BW
GSE231422_Coverage_FLI1_CMP_merge_clip.bw 217.9 Mb (ftp)(http) BW
GSE231422_Coverage_FLI1_GMP_merge_clip.bw 174.2 Mb (ftp)(http) BW
GSE231422_Coverage_FLI1_HSC.bw 165.4 Mb (ftp)(http) BW
GSE231422_Coverage_FLI1_MEP_merge_clip.bw 219.6 Mb (ftp)(http) BW
GSE231422_Coverage_GATA2_CMP_merge_clip.bw 198.3 Mb (ftp)(http) BW
GSE231422_Coverage_GATA2_GMP_merge_clip.bw 181.3 Mb (ftp)(http) BW
GSE231422_Coverage_GATA2_HSC.bw 165.9 Mb (ftp)(http) BW
GSE231422_Coverage_GATA2_MEP_merge_clip.bw 218.6 Mb (ftp)(http) BW
GSE231422_Coverage_H3K27me3_CMP.bw 110.4 Mb (ftp)(http) BW
GSE231422_Coverage_H3K27me3_GMP.bw 130.9 Mb (ftp)(http) BW
GSE231422_Coverage_H3K27me3_HSC.bw 128.4 Mb (ftp)(http) BW
GSE231422_Coverage_H3K27me3_MEP.bw 161.5 Mb (ftp)(http) BW
GSE231422_Coverage_LMO2_CMP_merge_clip.bw 218.0 Mb (ftp)(http) BW
GSE231422_Coverage_LMO2_GMP_clip.bw 214.9 Mb (ftp)(http) BW
GSE231422_Coverage_LMO2_HSC.bw 182.1 Mb (ftp)(http) BW
GSE231422_Coverage_LMO2_MEP_merge_clip.bw 216.4 Mb (ftp)(http) BW
GSE231422_Coverage_LYL1_CMP_merge_clip.bw 204.5 Mb (ftp)(http) BW
GSE231422_Coverage_LYL1_GMP_clip.bw 170.5 Mb (ftp)(http) BW
GSE231422_Coverage_LYL1_HSC.bw 163.0 Mb (ftp)(http) BW
GSE231422_Coverage_LYL1_MEP_merge_clip.bw 206.4 Mb (ftp)(http) BW
GSE231422_Coverage_PU1_CMP_merge_clip.bw 215.2 Mb (ftp)(http) BW
GSE231422_Coverage_PU1_GMP_clip.bw 176.9 Mb (ftp)(http) BW
GSE231422_Coverage_PU1_HSC.bw 194.8 Mb (ftp)(http) BW
GSE231422_Coverage_PU1_MEP_merge_clip.bw 210.3 Mb (ftp)(http) BW
GSE231422_Coverage_Pol2_CMP_clip_merge.bw 150.8 Mb (ftp)(http) BW
GSE231422_Coverage_Pol2_GMP_merge.bw 195.6 Mb (ftp)(http) BW
GSE231422_Coverage_Pol2_HSC_merge_clip.bw 220.3 Mb (ftp)(http) BW
GSE231422_Coverage_Pol2_MEP_merge_clip.bw 158.1 Mb (ftp)(http) BW
GSE231422_Coverage_RUNX1_CMP_merge_clip.bw 194.2 Mb (ftp)(http) BW
GSE231422_Coverage_RUNX1_GMP_merge_clip.bw 177.2 Mb (ftp)(http) BW
GSE231422_Coverage_RUNX1_HSC.bw 170.3 Mb (ftp)(http) BW
GSE231422_Coverage_RUNX1_MEP_merge_clip.bw 233.8 Mb (ftp)(http) BW
GSE231422_Coverage_STAG2_CMP_merge_clip.bw 165.6 Mb (ftp)(http) BW
GSE231422_Coverage_STAG2_GMP_merge_clip.bw 107.6 Mb (ftp)(http) BW
GSE231422_Coverage_STAG2_HSC.bw 208.8 Mb (ftp)(http) BW
GSE231422_Coverage_STAG2_MEP_merge_clip.bw 160.2 Mb (ftp)(http) BW
GSE231422_Coverage_TAL1_CMP_merge_clip.bw 197.5 Mb (ftp)(http) BW
GSE231422_Coverage_TAL1_GMP_merge_clip.bw 217.8 Mb (ftp)(http) BW
GSE231422_Coverage_TAL1_HSC.bw 163.4 Mb (ftp)(http) BW
GSE231422_Coverage_TAL1_MEP_merge_clip.bw 232.4 Mb (ftp)(http) BW
GSE231422_ERG_CMP_peaks.narrowPeak.gz 83.7 Kb (ftp)(http) NARROWPEAK
GSE231422_ERG_GMP_peaks.narrowPeak.gz 71.9 Kb (ftp)(http) NARROWPEAK
GSE231422_ERG_HSC_peaks.narrowPeak.gz 213.5 Kb (ftp)(http) NARROWPEAK
GSE231422_ERG_MEP_peaks.narrowPeak.gz 20.3 Kb (ftp)(http) NARROWPEAK
GSE231422_FLI1_CMP_peaks.narrowPeak.gz 644.9 Kb (ftp)(http) NARROWPEAK
GSE231422_FLI1_GMP_peaks.narrowPeak.gz 546.4 Kb (ftp)(http) NARROWPEAK
GSE231422_FLI1_HSC_peaks.narrowPeak.gz 185.1 Kb (ftp)(http) NARROWPEAK
GSE231422_FLI1_MEP_peaks.narrowPeak.gz 478.8 Kb (ftp)(http) NARROWPEAK
GSE231422_GATA2_CMP_peaks.narrowPeak.gz 437.7 Kb (ftp)(http) NARROWPEAK
GSE231422_GATA2_GMP_peaks.narrowPeak.gz 340.8 Kb (ftp)(http) NARROWPEAK
GSE231422_GATA2_HSC_peaks.narrowPeak.gz 281.2 Kb (ftp)(http) NARROWPEAK
GSE231422_GATA2_MEP_peaks.narrowPeak.gz 423.1 Kb (ftp)(http) NARROWPEAK
GSE231422_IgG_all4subfractions.bw 220.3 Mb (ftp)(http) BW
GSE231422_LMO2_CMP_peaks.narrowPeak.gz 232.0 Kb (ftp)(http) NARROWPEAK
GSE231422_LMO2_GMP_peaks.narrowPeak.gz 485.4 Kb (ftp)(http) NARROWPEAK
GSE231422_LMO2_HSC_peaks.narrowPeak.gz 138.3 Kb (ftp)(http) NARROWPEAK
GSE231422_LMO2_MEP_peaks.narrowPeak.gz 565.8 Kb (ftp)(http) NARROWPEAK
GSE231422_LYL1_CMP_peaks.narrowPeak.gz 230.4 Kb (ftp)(http) NARROWPEAK
GSE231422_LYL1_GMP_peaks.narrowPeak.gz 274.3 Kb (ftp)(http) NARROWPEAK
GSE231422_LYL1_HSC_peaks.narrowPeak.gz 238.4 Kb (ftp)(http) NARROWPEAK
GSE231422_LYL1_MEP_peaks.narrowPeak.gz 346.7 Kb (ftp)(http) NARROWPEAK
GSE231422_PU1_CMP_peaks.narrowPeak.gz 512.2 Kb (ftp)(http) NARROWPEAK
GSE231422_PU1_GMP_peaks.narrowPeak.gz 336.4 Kb (ftp)(http) NARROWPEAK
GSE231422_PU1_HSC_peaks.narrowPeak.gz 105.0 Kb (ftp)(http) NARROWPEAK
GSE231422_PU1_MEP_peaks.narrowPeak.gz 91.8 Kb (ftp)(http) NARROWPEAK
GSE231422_Pol2_CMP_peaks.narrowPeak.gz 243.2 Kb (ftp)(http) NARROWPEAK
GSE231422_Pol2_GMP_peaks.narrowPeak.gz 361.9 Kb (ftp)(http) NARROWPEAK
GSE231422_Pol2_HSC_peaks.narrowPeak.gz 457.2 Kb (ftp)(http) NARROWPEAK
GSE231422_Pol2_MEP_peaks.narrowPeak.gz 35.0 Kb (ftp)(http) NARROWPEAK
GSE231422_RUNX1_CMP_peaks.narrowPeak.gz 401.4 Kb (ftp)(http) NARROWPEAK
GSE231422_RUNX1_GMP_peaks.narrowPeak.gz 413.1 Kb (ftp)(http) NARROWPEAK
GSE231422_RUNX1_HSC_peaks.narrowPeak.gz 214.8 Kb (ftp)(http) NARROWPEAK
GSE231422_RUNX1_MEP_peaks.narrowPeak.gz 304.9 Kb (ftp)(http) NARROWPEAK
GSE231422_STAG2_CMP_peaks.narrowPeak.gz 138.7 Kb (ftp)(http) NARROWPEAK
GSE231422_STAG2_GMP_peaks.narrowPeak.gz 148.3 Kb (ftp)(http) NARROWPEAK
GSE231422_STAG2_HSC_peaks.narrowPeak.gz 302.5 Kb (ftp)(http) NARROWPEAK
GSE231422_STAG2_MEP_peaks.narrowPeak.gz 240.0 Kb (ftp)(http) NARROWPEAK
GSE231422_TAL1_CMP_peaks.narrowPeak.gz 103.4 Kb (ftp)(http) NARROWPEAK
GSE231422_TAL1_GMP_peaks.narrowPeak.gz 73.8 Kb (ftp)(http) NARROWPEAK
GSE231422_TAL1_HSC_peaks.narrowPeak.gz 99.4 Kb (ftp)(http) NARROWPEAK
GSE231422_TAL1_MEP_peaks.narrowPeak.gz 307.8 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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