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Series GSE60749 Query DataSets for GSE60749
Status Public on Dec 04, 2014
Title Deconstructing the dynamic transcriptional program of pluripotent stem cells.
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Pluripotent stem cells (PSCs) are capable of dynamic interconversion between distinct substates, but the regulatory circuits specifying these states and enabling transitions between them are not well understood. We set out to address this issue and map the landscape of gene expression variability in PSCs by single-cell expression profiling of PSCs under different chemical and genetic perturbations. We find that signaling factors and developmental regulators show highly variable expression in PSCs, with expression states for some variable genes heritable through multiple cell divisions. Expression variability and population heterogeneity can be influenced by perturbation of signaling pathways and chromatin regulators. Strikingly, either removal of mature miRNAs or pharmacologic blockage of external signaling pathways drives PSCs into a low-noise ground state characterized by a reconfigured pluripotency regulatory network, increased self-renewal efficiency, and a distinct chromatin state, an effect mediated by the action of opposing miRNA families on the c-myc / Lin28 / let-7 axis. These findings illuminate the causes of transcriptional heterogeneity in PSCs and their consequences for cellular decision-making.
 
Overall design Single-cell RNA-Seq on 183 individual v6.5 mouse embryonic stem cells (mESCs) cultured in serum+LIF media, 94 v6.5 mESCs cultured in 2i+LIF media ('ground state' conditions), and 84 Dgcr8 -/- mESCs (constructed in a v6.5 background), that lack mature miRNAs due to knockout of a miRNA processing factor, cultured in serum+LIF. ChIP-Seq for RNA polymerase II, H3K4me3, H3K27me3, H3K27ac, H3K9me3, and H3K36me3 on the three populations of mESCs profiled by single-cell RNA-Seq. Single-cell RNA-Seq on 54 individual nestin-positive neural precursor cells derived from v6.5 mESCs.
 
Contributor(s) Kumar RM, Cahan P
Citation(s) 25471879
Submission date Aug 26, 2014
Last update date Mar 21, 2019
Contact name Patrick Cahan
E-mail patrick.cahan@jhmi.edu
Organization name Johns Hopkins University School of Medicine
Department ICE and Biomedical Engineering
Lab Cahan Lab
Street address 733 North Broadway, MRB 653
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (441)
GSM1486634 FBSLIF_Plate1_A1
GSM1486635 FBSLIF_Plate1_B7
GSM1486636 FBSLIF_Plate1_A2
Relations
BioProject PRJNA259420
SRA SRP045775

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
GSE60749_ChIP_Seq_population_mESC.csv.gz 1004.4 Kb (ftp)(http) CSV
GSE60749_RnaSeq_population_mESC_TPM.csv.gz 435.6 Kb (ftp)(http) CSV
GSE60749_RnaSeq_single_cell_NPC_TPM.csv.gz 2.2 Mb (ftp)(http) CSV
GSE60749_RnaSeq_single_cell_mESC_TPM.csv.gz 14.1 Mb (ftp)(http) CSV
Processed data is available on Series record
Raw data are available in SRA

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