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Series GSE122791 Query DataSets for GSE122791
Status Public on Nov 22, 2018
Title The Type I interferon response impairs differentiation potential of pluripotent stem cells [seq]
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Upon virus infection,pluripotent stem cells neither induce nor respond to canonical Type I interferons (IFN-I). To better understand this biology,we characterized induced pluripotent stem cells (iPSCs) as well as their differentiated parental or re-derived counterparts. We confirmed that only iPSCs failed to respond to viral RNA,Type I interferon (IFN-I),or viral infection. This lack of response could be phenocopied in fibroblasts with the expression of a reprogramming factor which repressed the capacity to induce canonical antiviral pathways. To ascertain the consequences of restoring the antiviral response in the context of pluripotency,we engineered a system to engage these defenses in iPSCs. Inducible expression of a recombinant virus-activated transcription factor resulted in the successful reconstitution of antiviral defenses through the direct upregulation of IFN-I stimulated genes. Induction of the antiviral signature in iPSCs,even for a short duration,resulted in the dysregulation of genes associated with all three germ layers despite maintaining pluripotency markers. Trilineage differentiation of these same cells showed that engagement of the antiviral defenses compromised ectoderm and endoderm formation and dysregulated the development of mesodermal sublineages. In all,these data suggest that the temporal induction of the antiviral response primes iPSCs away from pluripotency and induces numerous aberrant gene products upon differentiaton. Together these results suggest that the IFN-I system and pluripotency may be incompatible with each other and thus explain why stem cells do not utilize the canonical antiviral system.
 
Overall design RNA-Seq data in duplicate for 70 total samples
 
Contributor(s) Eggenberger J, tenOever B
Citation(s) 30606801
Submission date Nov 21, 2018
Last update date Mar 26, 2019
Contact name Julie Anne Eggenberger
E-mail(s) julie.eggenberger@icahn.mssm.edu
Organization name Icahn School of Medicine at Mount Sinai
Department Microbiology
Lab tenOever Lab
Street address 1 Gustave L. Levy Pl
City New York
State/province NY
ZIP/Postal code 10029
Country USA
 
Platforms (3)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (76)
GSM3485419 FF-2 [Sample 1]
GSM3485420 FF-2 [Sample 2]
GSM3485421 iPS-1 [Sample 3]
This SubSeries is part of SuperSeries:
GSE122794 The Type I interferon response impairs differentiation potential of pluripotent stem cells
Relations
BioProject PRJNA506373
SRA SRP170013

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
GSE122791_TableS10_Primers.xlsx.gz 8.1 Kb (ftp)(http) XLSX
GSE122791_TableS1_PCA_Data.xlsx.gz 934.4 Kb (ftp)(http) XLSX
GSE122791_TableS1_read_counts.xlsx.gz 940.0 Kb (ftp)(http) XLSX
GSE122791_TableS2_miRNA_reads.xlsx.gz 152.5 Kb (ftp)(http) XLSX
GSE122791_TableS2_pppRNA_treated_FF.xlsx.gz 49.5 Kb (ftp)(http) XLSX
GSE122791_TableS2_pppRNA_treated_iPS.xlsx.gz 11.7 Kb (ftp)(http) XLSX
GSE122791_TableS2_pppRNA_treated_reFF.xlsx.gz 51.8 Kb (ftp)(http) XLSX
GSE122791_TableS3_Differential_expression.xlsx.gz 1.2 Mb (ftp)(http) XLSX
GSE122791_TableS3_conservedISG_RPM.xlsx.gz 8.4 Kb (ftp)(http) XLSX
GSE122791_TableS3_read_counts.xlsx.gz 1.5 Mb (ftp)(http) XLSX
GSE122791_TableS4_DEseq_GFP_vs_IRF7.xlsx.gz 1.4 Mb (ftp)(http) XLSX
GSE122791_TableS4_DEseq_GFP_vs_IRF7_KLF4.xlsx.gz 1.5 Mb (ftp)(http) XLSX
GSE122791_TableS4_DEseq_GFP_vs_KLF4.xlsx.gz 1.5 Mb (ftp)(http) XLSX
GSE122791_TableS4_Differential_IRF7_to_GFP.xlsx.gz 35.6 Kb (ftp)(http) XLSX
GSE122791_TableS4_read_counts_I.xlsx.gz 1.2 Mb (ftp)(http) XLSX
GSE122791_TableS4_read_counts_II.xlsx.gz 810.7 Kb (ftp)(http) XLSX
GSE122791_TableS5_Differential_iPSC_IRF7vGFP_48h.xlsx.gz 40.2 Kb (ftp)(http) XLSX
GSE122791_TableS5_iPSC_IRF7vGFP_48h_STRING.xlsx.gz 32.4 Kb (ftp)(http) XLSX
GSE122791_TableS5_read_counts.xlsx.gz 807.1 Kb (ftp)(http) XLSX
GSE122791_TableS6_Differential_iPSC_IRF7vGFP_rest.xlsx.gz 98.4 Kb (ftp)(http) XLSX
GSE122791_TableS6_iPSC_IRF7vGFP_rest_STRING.xlsx.gz 64.4 Kb (ftp)(http) XLSX
GSE122791_TableS6_read_counts.xlsx.gz 805.3 Kb (ftp)(http) XLSX
GSE122791_TableS7_DE_mES_IRF9VPRvGFP_12h.xlsx.gz 18.0 Kb (ftp)(http) XLSX
GSE122791_TableS7_DE_mES_IRF9VPRvGFP_rest.xlsx.gz 7.2 Kb (ftp)(http) XLSX
GSE122791_TableS7_read_counts_I.xlsx.gz 799.2 Kb (ftp)(http) XLSX
GSE122791_TableS7_read_counts_II.xlsx.gz 785.7 Kb (ftp)(http) XLSX
GSE122791_TableS8_allsamples_RPKM.xlsx.gz 5.0 Mb (ftp)(http) XLSX
GSE122791_TableS8_read_counts.xlsx.gz 2.3 Mb (ftp)(http) XLSX
GSE122791_TableS9_CMdiff_allsamples_RPKM.xlsx.gz 3.2 Mb (ftp)(http) XLSX
GSE122791_TableS9_read_counts.xlsx.gz 1.6 Mb (ftp)(http) XLSX
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