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SRP166074
Mus musculus
4 Downloadable Samples
Illumina HiSeq 2500
Description
Totipotency is defined as the ability of a cell to generate all the cell types of an organism, including those of the extraembryonic tissues. Unlike pluripotency, the molecular features and the establishment of totipotency are poorly understood. In mouse embryonic stem cell (ESC) culture, a small percentage of cells transits into a totipotent state by expressing a group of genes that are only expressed in 2-cell-stage embryos. To understand how this transition takes place, we performed single cell RNA-seq analysis which revealed a two-step transcriptional reprogramming process characterized by downregulation of pluripotent genes in the first step and upregulation of the 2-cell embryo-specific genes in the second step. To identify factors controlling the transition process, we performed a CRISPR/Cas9-mediated genetic screen which revealed Myc and Dnmt1 as two factors preventing the transition. Mechanistic studies demonstrate that Myc prevents down-regulation of the genes in the first step, while Dnmt1 impedes gene activation in the second step. Collectively, our study reveals insights into the mechanism underlying establishment and regulation of totipotent state in ESCs. Overall design: Here we performed bulk RNA-seq on ESC, D1 2C-negative, and D1 2C-positive cells. And performed single cell RNA-seq on Dux-induced ESC at 0h, 12h, 24h, and 36h. In addition, we performed bulk RNA-seq on sgGFP, sgDnmt1, sgMyc ESCs before and after Dux induction. Last, we performed RRBS on sgGFP and sgDnmt1 ESCs before and after Dux induction.
Publication Title
Myc and Dnmt1 impede the pluripotent to totipotent state transition in embryonic stem cells.
Sample Metadata Fields
Specimen part, Cell line, Subject, Time
View Samples- Homo sapiens
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
These RNA-seq data were generated to correlate with genomic interaction data in a related Hi-C analysis. Analysis revealed differential expressed genes in ATRA treated and control HL-60 cells. Changes of gene expression with topological associated domains (TADs) were showd to be correlated with chromatin structure alteration Overall design: HL-60 cells with ATRA or ethanol treated for 4 days were used to generate RNA-seq library, in replicate.
Publication Title
Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation.
Sample Metadata Fields
Specimen part, Disease, Cell line, Subject
View Samples- Mus musculus
- 18 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Effects of IL-4 on CD8 T cells functions are largely unknown. IL-4 induces survival and proliferation of CD8 T cells, but several studies suggest that IL-4 could also affect several functions of CD8 T cells such as cytotoxicity. Our team has shown that IL-4 repress the expression of Ccl5 in vitro.
Publication Title
Negative regulation of NKG2D expression by IL-4 in memory CD8 T cells.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We used Affymetrix expression arrays to determine changes in gene expression associated with activation of human NK cells mediated through treatment with cytokines IL-2, IL-12 and IL-18 over a 24 hour period.
Publication Title
PRDM1/Blimp-1 controls effector cytokine production in human NK cells.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 20 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Introduction
Publication Title
Frequent PTEN genomic alterations and activated phosphatidylinositol 3-kinase pathway in basal-like breast cancer cells.
Sample Metadata Fields
Sex, Disease stage
View Samples- Mus musculus
- 40 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Transcriptome analysis comparing naive, protective and non-protective spleen memory CD8 T lymphocytes were conducted to identify key functions associated with memory CD8-mediated immune protection. Memory CD8 T cells generated in response to influenza or vaccinia infection (Flu-memory and VV-memory) were compared to inflammatory memory cells (TIM) that were generated by peptide in inflammatory context. Gene expression analysis was performed on quiescent and re-stimulated CD8 T cells.
Publication Title
Immune signatures of protective spleen memory CD8 T cells.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 70 Downloadable Samples
- IlluminaHiSeq2000
Description
The FANTOM5 promoter expression atlas provides a rich source of expression and functional annotation of human and mouse cell-type specific transcriptomes with wide applications in biomedical research.
Publication Title
An atlas of human long non-coding RNAs with accurate 5' ends.
Sample Metadata Fields
No sample metadata fields
View Samples