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Series GSE160764 Query DataSets for GSE160764
Status Public on Dec 31, 2022
Title Epigenetic signals that direct cell type specific interferon beta response in mouse cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The antiviral response induced by type I interferon (IFN) via the JAK-STAT signaling cascade results in the activation of a set of IFN-stimulated genes (ISGs). This response varies between different cell types of the organism. However, the linkage between the underlying epigenetic features and innate immune response is not well understood. We mapped ISGs and STAT1 and STAT2 binding sites in mouse embryonic stem cells and differentiated cells before and after treatment with IFNβ together with histone acetylation (ac) and mono- and tri-methylation (me1, me3) marks at histone H3 lysine residues for H3K4me1, H3K4me3, H3K9ac, H3K27ac, H3K9me3 and H3K27me3. Many ISGs were cell type specific and displayed distinct STAT1/2 binding patterns at promoters. Furthermore, binding to putative enhancers at intergenic and intronic site was driving ISGs as inferred from a co-regulation analysis of open chromatin sites in single cells. Activator binding was dependent on the chromatin context and positively correlated with pre-existing H3K4me1 enrichment and open chromatin states while the presence of H3K27me3 had the opposite effect. Chromatin features present before stimulation direct the cell type specific response to type I IFNs. Thus, epigenetic signals represent an additional regulatory layer that is responsible for the tissue dependent activity of this signaling pathway. The mechanistic insight gained in our study could be exploited for modulating innate immune response during virus infection or cancer immunotherapy.
Overall design RNA-seq, ChIP-seq, ATAC-seq, scRNA-seq and scATAC-seq of mouse embryonic stem cells compared to mouse embryonic fibroblasts and differentiated neuronal progenitor cells upon interferon beta treatment

Please note that processed data files generated from multiple samples are linked as Series supplementary files, along with 'readme.txt' describing the data.
Web link
Contributor(s) Muckenhuber M, Seufert I, Rippe K
Citation(s) 36732019
Submission date Nov 03, 2020
Last update date Apr 12, 2023
Contact name Markus Muckenhuber
Organization name DKFZ
Lab AG Rippe
Street address Im Neuenheimer Feld 280
City Heidelberg
ZIP/Postal code 69120
Country Germany
Platforms (3)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (221)
GSM4878694 ATAC_ESC_Ola_IFNb_0h_Rep1
GSM4878695 ATAC_ESC_Ola_IFNb_0h_Rep2
GSM4878696 ATAC_ESC_Ola_IFNb_1h_Rep1
BioProject PRJNA674372
SRA SRP291015

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
GSE160764_ChIP_peaks_ESC_DiffBind_result_table_STAT1p701_and_STAT2_at_1h_and_6h.bed.gz 2.0 Kb (ftp)(http) BED
GSE160764_ChIP_peaks_ESC_DiffBind_result_table_STAT1p701_only_at_1h_and_6h.bed.gz 8.4 Kb (ftp)(http) BED
GSE160764_ChIP_peaks_ESC_DiffBind_result_table_STAT2_only_at_1h_and_6h.bed.gz 379 b (ftp)(http) BED
GSE160764_ChIP_peaks_MEF_DiffBind_result_table_STAT1p701_and_STAT2_at_1h_and_6h.bed.gz 2.9 Kb (ftp)(http) BED
GSE160764_ChIP_peaks_MEF_DiffBind_result_table_STAT1p701_only_at_1h_and_6h.bed.gz 1.5 Kb (ftp)(http) BED
GSE160764_ChIP_peaks_MEF_DiffBind_result_table_STAT2_only_at_1h_and_6h.bed.gz 2.6 Kb (ftp)(http) BED
GSE160764_Norm_count_table_ESC_Ola_ATAC_reads_at_STAT1p701_and_STAT2_peaks_at_1h_and_6h.txt.gz 10.9 Kb (ftp)(http) TXT
GSE160764_Norm_count_table_ESC_Ola_ChIP_reads_at_STAT1p701_and_STAT2_peaks_at_1h_and_6h.txt.gz 36.5 Kb (ftp)(http) TXT
GSE160764_Norm_count_table_MEF_Ola_ATAC_reads_at_STAT1p701_and_STAT2_peaks_at_1h_and_6h.txt.gz 11.0 Kb (ftp)(http) TXT
GSE160764_Norm_count_table_MEF_Ola_ChIP_reads_at_STAT1p701_and_STAT2_peaks_at_1h_and_6h.txt.gz 14.1 Kb (ftp)(http) TXT
GSE160764_RAW.tar 9.2 Gb (http)(custom) TAR (of BED, MTX, TAR, TSV)
GSE160764_RNA_ESC_Ola_IFNb_Counttable_Raw.txt.gz 809.6 Kb (ftp)(http) TXT
GSE160764_RNA_ESC_Ola_IFNb_Counttable_TPM_FPKM.txt.gz 2.4 Mb (ftp)(http) TXT
GSE160764_RNA_MEF_Ola_IFNb_Counttable_Raw.txt.gz 484.6 Kb (ftp)(http) TXT
GSE160764_RNA_MEF_Ola_IFNb_Counttable_TPM_FPKM.txt.gz 1.6 Mb (ftp)(http) TXT
GSE160764_RNA_NPC_Ola_IFNb_Counttable_Raw.txt.gz 720.9 Kb (ftp)(http) TXT
GSE160764_RNA_NPC_Ola_IFNb_Counttable_TPM_FPKM.txt.gz 2.2 Mb (ftp)(http) TXT
GSE160764_Table_DeSeq2_results_all_genes_1h_vs_0h_RNA_ESC_Ola_IFNb_padj_0.05_log2fc_0.585.txt.gz 2.2 Mb (ftp)(http) TXT
GSE160764_Table_DeSeq2_results_all_genes_1h_vs_0h_RNA_MEF_Ola_IFNb_padj_0.05_log2fc_0.585.txt.gz 1.3 Mb (ftp)(http) TXT
GSE160764_Table_DeSeq2_results_all_genes_1h_vs_0h_RNA_NPC_Ola_IFNb_padj_0.05_log2fc_0.585.txt.gz 1.7 Mb (ftp)(http) TXT
GSE160764_Table_DeSeq2_results_all_genes_6h_vs_0h_RNA_ESC_Ola_IFNb_padj_0.05_log2fc_0.585.txt.gz 2.3 Mb (ftp)(http) TXT
GSE160764_Table_DeSeq2_results_all_genes_6h_vs_0h_RNA_MEF_Ola_IFNb_padj_0.05_log2fc_0.585.txt.gz 1.3 Mb (ftp)(http) TXT
GSE160764_Table_DeSeq2_results_all_genes_6h_vs_0h_RNA_NPC_Ola_IFNb_padj_0.05_log2fc_0.585.txt.gz 1.7 Mb (ftp)(http) TXT
GSE160764_Table_DeSeq2_results_all_genes_6h_vs_1h_RNA_ESC_Ola_IFNb_padj_0.05_log2fc_0.585.txt.gz 2.3 Mb (ftp)(http) TXT
GSE160764_Table_DeSeq2_results_all_genes_6h_vs_1h_RNA_MEF_Ola_IFNb_padj_0.05_log2fc_0.585.txt.gz 1.3 Mb (ftp)(http) TXT
GSE160764_Table_DeSeq2_results_all_genes_6h_vs_1h_RNA_NPC_Ola_IFNb_padj_0.05_log2fc_0.585.txt.gz 1.7 Mb (ftp)(http) TXT
GSE160764_readme.txt 11.2 Kb (ftp)(http) TXT
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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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