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Single cell RNA sequencing data of embryonal carcinoma cells in vitro differentiated into yolk-sac tumor-like cells

ABSTRACT: Single cell RNA sequencing data of embryonal carcinoma cells in vitro differentiated into yolk-sac tumor-like cells

PROVIDER: PRJNA1006320 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25663023_1.fastq.gz	Fastqsanger.gz
	SRR25663023_2.fastq.gz	Fastqsanger.gz
	SRR25663024_1.fastq.gz	Fastqsanger.gz
	SRR25663024_2.fastq.gz	Fastqsanger.gz
	SRR25663025_1.fastq.gz	Fastqsanger.gz

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Single cell RNA sequencing data of embryonal carcinoma cells in vitro differentiated into yolk-sac tumor-like cells

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Project description:GW182 (Tnrc6a) is a key component of RISC (miRNA-Induced Silencing Complex) that plays a critical role in miRNA-mediated gene silencing. Here, we show that GW182 is expressed in the yolk sac endoderm, and that gene-trap disruption of GW182 leads to growth arrest of yolk sac endoderm, impaired hematopoiesis and embryonic lethality. To investigate roles of GW182 in the yolk sac endoderm, we assessed changes in mRNA expression in the yolk sac of E9.5 GW182gt/gt embryos using microarrays (Affymetrix). Yolk sac of wild type littermates and GW182gt/gt embryos at E9.5 was collected for total RNA isolation using Trizol (Invitrogen). RNAs were purified according to the manufacturer’s protocol before subjected to Mouse Gene 1.0 ST Whole Genome Array (Affymetrix) for mRNA expression profiling. Experiments were performed in triplicate. Differentially expressed mRNAs were identified using a two-sample t-test (P<0.05 considered significant).

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Project description:The human yolk sac (YS) is an extra-embryonic tissue critical for early prenatal life development. It is the first site of haematopoiesis where progenitors differentiate from endoderm within blood islands of the yolk sac contributing initially to primitive erythropoiesis and in subsequent waves to erythro-myeloid and lymphoid differentiation.

2023-03-01 | E-MTAB-10552 | biostudies-arrayexpress

Human fetal yolk sac scRNA-seq data (sample ID: F158 for Haniffa Lab; 16099 for HDBR)

Project description:Investigating the blood, immune and stromal cells present in a human fetal embryo in a world first single cell transcriptomic atlas. The embryo was dissected into 12 coronal sections, yolk sac, and yolk sac stalk. Live single cells sorted, with cell suspension then undergoing 10x chromium 5 prime scRNA-seq. This accession contains the yolk sac and yolk sac stalk data from this embryo. A matched accession contains the coronal section data. Lane "WS_wEMB12142156" (from yolk sac) was excluded from downstream analysis due to low fraction reads in cells post-CellRanger QC. Termination procedure for this embryo was medical. The F158_[features...barcodes...matrix].[tsv...mtx].gz files attached to this accession represent raw count data from all the 10x lanes in this accession combined, and as output from CellRanger filtered matrices (CellRanger version 6.0.1 using human reference genome GRCh38-2020-A). One set of count matrices relates to the yolk sac data, and one set of count matrices relates to the yolk sac stalk data.

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Project description:Rudhira is essential for mouse developmental angiogenesis and tissue morphogenesis. Embryos lacking endothelial rudhira die at mid-gestation with vascular patterning defects. Rudhira mutant yolk sac endothelial cells show slow and random migration. So to identify key signaling pathways perturbed in the absence of rudhira, we undertook whole transcriptome based analysis of gene expression in rudhira null yolk sac and embryo. Transcriptome analysis shows that key mediators of angiogenesis, cell adhesion, migration and extracellular matrix degradation as well as several components of the TGFÎ² pathway are perturbed in rudhira null mutant yolk sacs at 9.5 dpc. We used two embryo samples ( 2E- wild type; 5E- rudhira mutant). Repetition was done on each sample. We used 4 yolk sac samples (3Y,4Y- wild type; 7Y,8Y-rudhira mutant) for the analysis. Repetition was done on each sample.

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