Single Cell RNA-seq time course of mouse gastruloids at 0h (mESCs), 24h, 48h and 72h post-aggregation
Ontology highlight
ABSTRACT:
INSTRUMENT(S): NextSeq 500
ORGANISM(S): Mus musculus
SUBMITTER: charles girardot
PROVIDER: E-MTAB-12749 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Comparative single cell transcriptomic study (using 10x Genomics v3.1 kits) of gastruloids, aggregates of mESCs, at different developmental timepoints. mESCs, corresponding to the 0h timepoint, were also sequenced. The source mESCs were grown in 2 distinct media conditions: DMEM-based Serum-LIF (SL), SL + 0.3uM PD03 (SL + 1i) and SL + 1.5uM CGP77 + 3uM CHIR99 (SL + a2i). The following sets of timepoints were compared: 0hpa (hours post-aggregation) SL, 0hpa SL + 1i, 0hpa SL + a2i (corresponding to the mESC timepoint; 48hpa SL, 48hpa SL + 1i, 72hpa SL + a2i (corresponding to the pre-CHIR99 timepoint); 72hpa SL, 72hpa SL + 1i, 96hpa SL + a2i (corresponding to the post-CHIR99 timepoint); 120hpa SL, 120hpa SL + 1i, 144hpa SL + a2i (corresponding to the maximum elongation timepoint). The aim of this study was to delineate whether mESC pluripotent state influences cell and tissue fate acquisition dynamics. Gastruloids used in this study were generated from a transgenic G4 mESC line (George et al., PNAS 2007) modified via CRISPR-Cas9 mediated heterozygous knock-in of a Bra/T reporter allele (p2a-H2B-eGFP) as well as a ubiquitous nuclear marker allele (CAG::H2B-mKO2).
2024-11-13 | E-MTAB-13643 | biostudies-arrayexpress
Project description:These datasets are test datasets of sample-multiplexed scRNA-seq, consisting of cDNA (transcriptome) and sample barcode read files: Three-sample multiplexing experiment (JS009) is a MULTI-seq dataset containing mesenchyme embryonic hind limb bud cells, embryonic stem (ES) cells, and NIH3T3 cells. Each cell sample was labelled with a distinct MULTI-seq barcode. The barcode sequences were, CATAGAGC, TCCTCGAA, and GTGTACCT for the limb bud mesenchyme cells, the ES cells, and the NIH3T3 cells, respectively. Two-sample multiplexing experiment (JS010) is a CellPlex detaset, containing ES cells and NIH3T3 cells. Each cell sample was labelled with the 3'CellPlex Kit (10X Genomics). NIH3T3 cells and ES cells were labelled with CMO301 and CMO302, respectively.
2024-01-09 | E-MTAB-13181 | biostudies-arrayexpress
Project description:Purpose: This study aimed at exploring the deregulated genes in setd2 knockout mESCs compared with wt, more particularly to find the mechanism controlled by setd2,which was required for endoderm differentiation. Methods: Setd2 wt and ko mESCs were generated by deep sequencing, using Illumina GAIIx. Using Avadis NGS (version:1.3) software to analyze the sequence reads that passed quality filter to acquire the expression level of all genes. qRT–PCR validation was performed usingSYBR Green assays. Results: Using an optimized data analysis workflow, we mapped about 80 million sequence reads per sample to the mouse genome (build mm9) and identified 17,827 transcripts in the sted2 wt and ko mESCs. About 2,516 genes were deregulated in setd2 ko mESCs, more than 10 genes were validated using qRT-PCR. Conclusions: Through RNA-seq,we noticed that a subset of genes that related to MAPK signaling pathways were down-regulated in ko mESCs. This provided a bridge to connect setd2 and mESCs endoderm differentiation. One wt and one ko mESCs were generated by deep sequencing, using Illumina GAIIx.
2014-10-14 | E-GEOD-54932 | biostudies-arrayexpress
Project description:SETD2/HYPB has been known as a histone H3K36 specific methyltransferase. However, its roles in physiology such as development and cellular function remain unclear. In this study, using mESCs as cellular model, we show that Setd2 mainly regulates differentiation of murine embryonic stem cells (mESCs) towards primitive endoderm. This study aimed at exploring how did Setd2 regulate primitive endoderm. differentiation. We used microarrays to detail the global programme of gene expression controled by setd2, which is required for endoderm differentiation. Wild type and Setd2 knockout mESCs were selected for RNA extraction and hybridization on Affymetrix GeneChip® mouse genome 430 2.0 arrays. We sought to obtain some deregulated genes, which were required for primitive endoderm differentiation. For comparison, three biological repeats of each were performed.
2014-10-14 | E-GEOD-54931 | biostudies-arrayexpress
Project description:Inactivating mutations in the MEN1 gene predisposing to the multiple endocrine neoplasia type 1 (MEN1) syndrome can also cause sporadic pancreatic endocrine tumors. MEN1 encodes menin, a subunit of MLL1/MLL2-containing histone methyltransferase complexes that trimethylate histone H3 at lysine 4 (H3K4me3). The importance of menin-dependent H3K4me3 in normal and transformed pancreatic endocrine cells is unclear. To study the role of menin-dependent H3K4me3, we performed in vitro differentiation of wild-type as well as menin-null mouse embryonic stem cells (mESCs) into pancreatic islet-like endocrine cells (PILECs). Gene expression analysis and genome-wide H3K4me3 ChIP-Seq profiling in wild-type and menin-null mESCs and PILECs revealed menin-dependent H3K4me3 at the imprinted Dlk1-Meg3 locus in mESCs, and all four Hox loci in differentiated PILECs. Specific and significant loss of H3K4me3 and gene expression was observed for genes within the imprinted Dlk1-Meg3 locus in menin-null mESCs and the Hox loci in menin-null PILECs. Given that the reduced expression of genes within the DLK1-MEG3 locus and the HOX loci is associated with MEN1-like sporadic tumors, our data suggests a possible role for menin-dependent H3K4me3 at these genes in the initiation and progression of sporadic pancreatic endocrine tumors. Furthermore, our investigation also demonstrates that menin-null mESCs can be differentiated in vitro into islet-like endocrine cells, underscoring the utility of menin-null mESC-derived specialized cell types for genome-wide high-throughput studies. Genome-wide mapping of H3K4me3 and microarray gene expression profiling in TC-1 wild-type (WT) mESCs, menin-null (Men1-ko) mESCs (3.2N), pancreatic islet-like endocrine cells (PILECs) derived from WT mESCs, and PILECs derived from Men1-ko mESCs.
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Project description:Mouse embryonic stem cells (mESCs), derived from pre-implantation blastocyst cells, can be maintained in vitro in defined N2B27 medium supplemented with two chemical inhibitors for GSK3 and MEK (2i) and the cytokine leukemia inhibitory factor (LIF), which act synergistically to promote self-renewal and pluripotency. Many efforts have been devoted to identify genes that promote exit from the pluripotent state and the transition to a primed state of differentiation. One of the first identified players in this process was the Wnt/b-catenin effector TCF7L1 (previously referred to as TCF3), belonging to the family of four TCF/LEF transcription factors, which acts as pro-differentiation factor by repressing pluripotency genes. Of note, there is little evidence that the genetic abrogation of the mechanisms required for the exit from the pluripotent state is sufficient to enable self-renewal in the absence of 2iL. Here, we found that complete loss-of-function of Tcf7, Lef1, Tcf7l1 and Tcf7l2, the genes encoding for the four TCF/LEF transcription factors, (refered to as qKO) allows mESCs to become fully 2iL-independent and to propagate in basal N2B27. To understand the genetic program that allows qKO cells to achieve 2iL-independent self-renewal, we performed RNA sequencing (RNA-seq) of qKO and wild type mESCs.
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Project description:Genome-wide occupancy of biotinylated Jmjd2b, Jmjd2c from mESCs, as well as occupancy of selected factors and histone marks from wild-type mESCs, Anti-GFP KD, Jmj2b KD and Jmjd2c KD mESCs genome To identify genome-wide binding target sites of Jmjd2b and Jmjd2c in the mESCs genome, and genome-wide binding sites for selected factors and histone marks from Anti-GFP KD, Jmjd2b KD and Jmjd2c KD mESCs
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