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Series GSE142468 Query DataSets for GSE142468
Status Public on Dec 31, 2020
Title Transcription factor TCF1 is indispensable for the epigenetic priming of EILPs toward distinct cell fates
Organism Mus musculus
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Summary Differentiation of Innate lymphoid cells (ILCs) from hematopoietic stem cells needs go through several progenitor stages defined by various cell surface markers. The progenitor populations at specific developmental stages may have multiple lineage potentials. However, it is not clear whether the multipotency of the progenitors are induced in situ by differentiation signals or are already predefined by epigenetic states. Here we report the profiling of genome-wide nucleosome position and chromatin accessibility simultaneously in ILC progenitors EILPs and ILCPs by single-cell MNase-Seq. We find that EILPs contain distinct sub-populations epigenetically primed toward either myeloid or ILC lineages, while ILCPs contain cells mainly primed for the ILC lineage at epigenetic level. We further demonstrate that the transcription factor TCF1 is indispensable for the epigenetic priming of lineage-defining sites (LDSs) for both myeloid lineages and ILC lineages at the EILP stage, and deletion of TCF1 results in the epigenetic priming that favors the myeloid lineages. Our results suggest that the multipotency of progenitor cells is defined by the existence of heterogeneous population of cells epigenetically primed for distinct downstream lineages, which are regulated by key transcription factors.
Overall design We performed scMNase-seq for wild-type EILPs, ILCPs, and Tcf7-deficient EILPs to profile nucleosome positions and chromatin accessibility in single cells for each cell type. We performed DNase-seq and ChIC-seq of H3K4me3, H3K27ac, and H3K27me3 for ALPs, EILPs, ILCPs and Tcf7-deficient EILPs to profile chromatin accessibility and histone modifications in bulk cells for each cell condition. We performed ChIC-seq of TCF1 for EILPs and ILCPs to profile TCF1 binding in bulk cells for each cell type.
Contributor(s) Ren G, Lai B, Harly C, Cui K, Bhandoola A, Zhao K
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Submission date Dec 20, 2019
Last update date May 11, 2022
Contact name Keji Zhao
Organization name NHLBI,NIH
Department Systems Biology Center
Lab Laboratory of Epigenome Biology
Street address 9000 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (902)
GSM4229110 ChIC-seq_TCF1_EILP_rep1_GB3039
GSM4229111 ChIC-seq_TCF1_EILP_rep2_GB3048
GSM4229112 ChIC-seq_TCF1_EILP_rep3_GB6236
BioProject PRJNA597214
SRA SRP238508

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
GSE142468_ALP_H3K27ac-W200-normalized.wig.gz 22.5 Mb (ftp)(http) WIG
GSE142468_ALP_H3K27me3-W200-normalized.wig.gz 18.6 Mb (ftp)(http) WIG
GSE142468_ALP_H3K4me3-W200-normalized.wig.gz 13.1 Mb (ftp)(http) WIG
GSE142468_ALP_IgG-W200-normalized.wig.gz 4.2 Mb (ftp)(http) WIG 20.7 Mb (ftp)(http) WIG 7.1 Mb (ftp)(http) WIG 20.1 Mb (ftp)(http) WIG 11.8 Mb (ftp)(http) WIG 8.7 Mb (ftp)(http) WIG 3.9 Mb (ftp)(http) WIG 11.7 Mb (ftp)(http) WIG 18.6 Mb (ftp)(http) WIG 27.0 Mb (ftp)(http) WIG 25.2 Mb (ftp)(http) WIG 4.2 Mb (ftp)(http) WIG
GSE142468_ILCP_H3K27ac-W200-normalized.wig.gz 20.7 Mb (ftp)(http) WIG
GSE142468_ILCP_H3K27me3-W200-normalized.wig.gz 18.0 Mb (ftp)(http) WIG
GSE142468_ILCP_H3K4me3-W200-normalized.wig.gz 8.7 Mb (ftp)(http) WIG
GSE142468_ILCP_IgG-W200-normalized.wig.gz 507.2 Kb (ftp)(http) WIG
GSE142468_ILCP_TCF1_GB8022.150l-W100-normalized.wig.gz 5.2 Mb (ftp)(http) WIG 21.0 Mb (ftp)(http) WIG
GSE142468_RAW.tar 700.3 Mb (http)(custom) TAR (of BED)
GSE142468_RPKM.xlsx 1.2 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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