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MRNA sequencing analysis during mouse trophoblast stem cells differentiation into trophoblast giant cells

ABSTRACT: mRNA sequencing analysis during mouse trophoblast stem cells differentiation into trophoblast giant cells

PROVIDER: PRJNA1026658 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26343906_1.fastq.gz	Fastqsanger.gz
	SRR26343906_2.fastq.gz	Fastqsanger.gz
	SRR26343907_1.fastq.gz	Fastqsanger.gz
	SRR26343907_2.fastq.gz	Fastqsanger.gz
	SRR26343908_1.fastq.gz	Fastqsanger.gz

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mRNA sequencing analysis during mouse trophoblast stem cells differentiation into trophoblast giant cells

Project description:We performed RNA-seq to determine the differential expression genes from undifferentiated trophoblast stem cells (TSCs) and 7-days differentiated trophoblast giant cells (TGCs). We performed RNA-seq to determine the differential expression genes from undifferentiated trophoblast stem cells (TSCs) and 7-days differentiated trophoblast giant cells (TGCs). mTSCs were nurtured in a stem cell medium specifically designed for their growth. The differentiation of mTSCs into TGCs were enabled using a specialized differentiation medium for 7-days. This medium was essentially SCM without the components of FGF4 and heparin.

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Project description:We characterized the mouse trophoblast giant cell epigenome and gene expression profiles. We then compared these data to our data on underrepresentation in the polyploid trophoblast giant cells. We profiled 5 histone modifications (+ chromatin input) using ChIP-Seq, and digital expression profiles (3' RNA-Seq) for trophoblast giant cells derived from mouse. Furthermore, we profiled digital expression profiles (3' RNA-Seq) for in vivo trophoblast giant cells samples from e9.5 wildtype mouse trophoblast giant cells. We found that underrepresented domains in trophoblast giant cells are enriched for repressive marks and anti-correlate with active marks and transcription.

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Project description:We characterized regions of underrepresentation that are specific to mouse polyploid trophoblast giant cells. We performed array Comparative Genomics Hybridization (aCGH) to examine copy number variation (CNV) in mouse polyploid trophoblast giant cells (TGCs). We performed the following experiments in duplicates to examine CNV during various stages of in vivo and in vitro TGC development: e9.5 TGCs vs. embryonic controls, e11.5 TGCs vs. embryonic controls, e13.5 TGCs vs. embryonic controls, e16.5 TGCs vs. embryonic controls, as well as TGCs cultured 3, 5 and 7 days vs. 2N trophoblast stem cells. We also performed the following controls to show that underrepresentation is only found in polypoid trophoblast giant cells and not in either 2N placental cell types nor in other types of polyploid cells: 2N placenta disk vs. embryonic controls, 2N trophoblast stem cells vs. embryonic stem cells, and polyploid Megakaryocytes vs. embryonic controls. When possible, we performed arrays with the test and control samples of opposite sex (F-female, M-male), as an internal control for the array.

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Project description:We profiled trophoblast stem cell replication-timing in order to compare these data to our data on underrepresented (UR) domainss in trophoblast giant cells (polyploid cells derived from 2N trophoblast stem cells). We found that UR domains are formed from late-replicating regions in tropoblast stem cells. Profile of early and late replicating regions in cultured trophoblast stem cells.

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