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Series GSE198730 Query DataSets for GSE198730
Status Public on Jul 31, 2022
Title Transcriptomics, Regulatory Syntax, and Enhancer Identification in Heterogenous Populations of Mesoderm-Induced ESCs at Single-Cell Resolution
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary ESCs can adopt lineage-specific gene expression programs by stepwise exposure to defined factors, resulting in the generation of functional cell types. Bulk and single cell-based assays were employed to catalogue gene expression, histone modifications, chromatin conformation and accessibility transitions in ESC populations and individual cells acquiring a presomitic mesoderm fate and undergoing further lineage specification. These assays identified cis-regulatory regions and transcription factors presiding gene expression programs occurring at defined ESC transitions and revealed the presence of heterogenous cell populations within discrete ESC developmental stages. The datasets were employed to identify previously unappreciated genomic elements directing the initial activation of Pax7 and myogenic and neurogenic gene expression programs. This study provides a resource for the discovery of genomic and transcriptional features of pluripotent, mesoderm-induced ESCs, and ESCs-derived cell lineages.
 
Overall design To catalogue gene expression, histone modifications, chromatin conformation and accessibility transitions in ESC populations and individual cells undergoing lineage specification. we induced ESCs differentiation and characterized their transcriptome and epigenome at specific developmental junctures. we examined genome wide , chromatin accessibilty and gene expression in both bulk and single cell in Naive ESC (Naive) (three replicates) and instructed ESC (Instructed), (two replicates). We characterized regulatory regions with active (H3K4me1 and H3K27ac, two replicates) epigenetic marks in Naive and instructed ESC. To gain insite on how chromatin accessibility remodelled and the transcriptionally heterogeneity of differntiated ESCs, we performed scATAC-seq and scRNAseq in ES-derived aPSM (aPSM) and multiomics in ES-derived HIFLR (HIFLR) . We then leveraged these datasets and, by combining chromatin accessibility, in situ Hi-C chromatin conformation in aPSM and HIFLR cells, genome editing, and reporter assays have identified regulatory regions directing initial Pax7 expression and activation of the myogenic and neurogenic programs.

Please note that 'HIFLR_snATAC_fragments.tsv.gz' file was included on Dec 6, 2022.
 
Contributor(s) Khateb M, Perovanovic J, Ko KD, Jiang K, Feng X, Luna Na, Chal J, Ciuffoli V, Genzor P, Haase A, Simone J, Pourquie O, Dell'Orso S, Sartorelli V
Citation(s)
  • Khateb M, Perovanovic J, Ko KD, Jiang K et al. Transcriptomics, regulatory syntax, and enhancer identification in mesoderm-induced ESCs at single-cell resolution. Cell Rep 2022 Aug 16;40(7):111219. PMID: 35977485
NIH grant(s)
Grant ID Grant title Affiliation Name
Z01 AR041126 Control of Myogenesis and Regulation of MyoD Post-Transcriptional Modifications National Institute of Arthritis and Musculoskeletal and Skin Diseases Vittorio Sartorelli
ZIA AR041164 SIRT1 in Skeletal Muscle Development, Regeneration, and Atrophy National Institute of Arthritis and Musculoskeletal and Skin Diseases Vittorio Sartorelli
Submission date Mar 15, 2022
Last update date Dec 22, 2022
Contact name Vittorio Sartorelli
Organization name NIH
Department NIAMS
Street address 50 South Dr.
City Bethsda
State/province MD
ZIP/Postal code 20814
Country USA
 
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21626 NextSeq 550 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (39)
GSM5955902 Naïve ESC- bulk RNAseq_rep1
GSM5955903 Naïve ESC- bulk RNAseq_rep2
GSM5955904 Naïve ESC- bulk RNAseq_rep3
Relations
BioProject PRJNA816557

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
GSE198730_BulkRNA_ANOVA.xlsx 1.9 Mb (ftp)(http) XLSX
GSE198730_BulkRNA_RPKM.xlsx 1.4 Mb (ftp)(http) XLSX
GSE198730_HIFLR_matrix_merged.hic 2.1 Gb (ftp)(http) HIC
GSE198730_HIFLR_snATAC_fragments.tsv.gz 2.9 Gb (ftp)(http) TSV
GSE198730_HIFLR_snATAC_fragments.tsv.gz.tbi.gz 1.2 Mb (ftp)(http) TBI
GSE198730_HIFLR_snRNA_barcodes.tsv.gz 74.6 Kb (ftp)(http) TSV
GSE198730_HIFLR_snRNA_features.tsv.gz 3.5 Mb (ftp)(http) TSV
GSE198730_HIFLR_snRNA_matrix.mtx.gz 648.4 Mb (ftp)(http) MTX
GSE198730_Instructed_ESC_H3K27Ac_rep1_peaks.bed.gz 320.7 Kb (ftp)(http) BED
GSE198730_Instructed_ESC_H3K27Ac_rep2_peaks.bed.gz 371.2 Kb (ftp)(http) BED
GSE198730_Instructed_ESC_H3K4me1_rep1_peaks.bed.gz 276.6 Kb (ftp)(http) BED
GSE198730_Instructed_ESC_H3K4me1_rep2_peaks.bed.gz 229.2 Kb (ftp)(http) BED
GSE198730_Instructed_ESC_bulkATAC_rep1_peaks.bed.gz 1.1 Mb (ftp)(http) BED
GSE198730_Instructed_ESC_bulkATAC_rep2_peaks.bed.gz 1.0 Mb (ftp)(http) BED
GSE198730_Instructed_ESC_scATAC_rep1_barcodes.tsv.gz 25.8 Kb (ftp)(http) TSV
GSE198730_Instructed_ESC_scATAC_rep1_filtered_peak_bc_matrix.h5 41.8 Mb (ftp)(http) H5
GSE198730_Instructed_ESC_scATAC_rep1_fragments.tsv.gz 643.5 Mb (ftp)(http) TSV
GSE198730_Instructed_ESC_scATAC_rep1_matrix.mtx.gz 69.4 Mb (ftp)(http) MTX
GSE198730_Instructed_ESC_scATAC_rep1_peaks.bed.gz 1.2 Mb (ftp)(http) BED
GSE198730_Instructed_ESC_scATAC_rep1_singlecell.csv.gz 3.4 Mb (ftp)(http) CSV
GSE198730_Instructed_ESC_scRNA_rep1_barcodes.tsv.gz 30.7 Kb (ftp)(http) TSV
GSE198730_Instructed_ESC_scRNA_rep1_features.tsv.gz 244.7 Kb (ftp)(http) TSV
GSE198730_Instructed_ESC_scRNA_rep1_matrix.mtx.gz 43.1 Mb (ftp)(http) MTX
GSE198730_Naive_ESC_H3K27Ac_rep1_peaks.bed.gz 276.7 Kb (ftp)(http) BED
GSE198730_Naive_ESC_H3K27Ac_rep2_peaks.bed.gz 302.0 Kb (ftp)(http) BED
GSE198730_Naive_ESC_H3K4me1_rep1_peaks.bed.gz 380.2 Kb (ftp)(http) BED
GSE198730_Naive_ESC_H3K4me1_rep2_peaks.bed.gz 348.6 Kb (ftp)(http) BED
GSE198730_Naive_ESC_bulkATAC_rep1_peaks.bed.gz 970.0 Kb (ftp)(http) BED
GSE198730_Naive_ESC_bulkATAC_rep2_peaks.bed.gz 1.3 Mb (ftp)(http) BED
GSE198730_Naive_ESC_scATAC_rep1_barcodes.tsv.gz 20.1 Kb (ftp)(http) TSV
GSE198730_Naive_ESC_scATAC_rep1_fragments.tsv.gz 836.2 Mb (ftp)(http) TSV
GSE198730_Naive_ESC_scATAC_rep1_matrix.mtx.gz 27.3 Mb (ftp)(http) MTX
GSE198730_Naive_ESC_scATAC_rep1_peaks.bed.gz 1.0 Mb (ftp)(http) BED
GSE198730_Naive_ESC_scATAC_rep1_singlecell.csv.gz 4.5 Mb (ftp)(http) CSV
GSE198730_Naive_ESC_scRNA_rep1_barcodes.tsv.gz 23.3 Kb (ftp)(http) TSV
GSE198730_Naive_ESC_scRNA_rep1_features.tsv.gz 244.7 Kb (ftp)(http) TSV
GSE198730_Naive_ESC_scRNA_rep1_matrix.mtx.gz 43.9 Mb (ftp)(http) MTX
GSE198730_Somites_bulkATAC_rep1_peaks.bed.gz 1.3 Mb (ftp)(http) BED
GSE198730_Somites_bulkATAC_rep2_peaks.bed.gz 1.2 Mb (ftp)(http) BED
GSE198730_aPSM_matrix_merged.hic 2.5 Gb (ftp)(http) HIC
GSE198730_aPSM_scATAC_rep1_barcodes.tsv.gz 20.1 Kb (ftp)(http) TSV
GSE198730_aPSM_scATAC_rep1_filtered_peak_bc_matrix.h5 23.0 Mb (ftp)(http) H5
GSE198730_aPSM_scATAC_rep1_fragments.tsv.gz 593.8 Mb (ftp)(http) TSV
GSE198730_aPSM_scATAC_rep1_matrix.mtx.gz 36.7 Mb (ftp)(http) MTX
GSE198730_aPSM_scATAC_rep1_peaks.bed.gz 713.9 Kb (ftp)(http) BED
GSE198730_aPSM_scATAC_rep1_singlecell.csv.gz 3.0 Mb (ftp)(http) CSV
GSE198730_aPSM_scRNA_rep1_barcodes.tsv.gz 30.5 Kb (ftp)(http) TSV
GSE198730_aPSM_scRNA_rep1_features.tsv.gz 244.7 Kb (ftp)(http) TSV
GSE198730_aPSM_scRNA_rep1_matrix.mtx.gz 65.0 Mb (ftp)(http) MTX
GSE198730_naive_ESC_scATAC_rep1_filtered_peak_bc_matrix.h5 20.7 Mb (ftp)(http) H5
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