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PolyA-tail enriched RNA-seq in differentiating TX1072 XX mESCs

ABSTRACT: PolyA-tail enriched RNA-seq in differentiating TX1072 XX mESCs

PROVIDER: PRJNA704376 | ENA |

REPOSITORIES: ENA

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PolyA-tail enriched RNA-seq in differentiating TX1072 XX mESCs

Project description:Developmental genes are controlled by complex cis-regulatory landscapes that integrate multiple signals to ensure the correct spatio-temporal expression pattern. To investigate the underlying regulatory principles, we use the Xist locus as a model, which encodes the master regulator of X-chromosome inactivation. Xist is upregulated at the primed pluripotent state in a female-specific manner, thus integrating developmental cues and X-dosage information. It remains poorly understood how these signals are decoded by the ~800kb genomic region that controls Xist. While a series of repressive cis-regulatory elements have been identified, the distal enhancers that activate Xist transcription remain largely unknown. Here we use polyA-tail enriched RNA-seq within the wildtype TX1072 XX cell line after two days of differentiation.

2021-03-04 | GSE167354 | GEO

RNA-seq in TX1072 XO mESCs during differentiation

Project description:RNA-seq in TX1072 XO mESCs during differentiation

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Smarca4 ChIP-seq in XX and XY mESCs

Project description:Smarca4 ChIP-seq in XX and XY mESCs

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RNA seq comparative analysis of XX, XY, and XXTet3-/- mutant mouse embryonic stem cells versus XX, XY, and XXTet3-/- mutant epiblast-like cells

Project description:In XXTet3-/- mESCs DNA methylation levels are higher than XX wildtype levels. We sought to determine if changes in cytosine modifications observed in XXTet3-/- mESCs impacted gene expression, we performed RNA-seq. 104 genes were up regulated in the mutant XX mESCs relative to wild type controls, and 86 were down regulated To ask whether the XX-specific nuclear enrichment of TET3 is necessary for a developmental transition, we differentiated WT XX and XXTet3-/- mESCs into epiblast-like cells (EpiLCs). Comparison of WT XX and XXTet3-/- EpiLC RNA-seq showed that 404 genes exhibited increased expression and 499 exhibited decreased expression in mutant cells. GO term analysis showed gene expression changes affecting several LIF and BMP signaling pathways. However, despite these changes in signaling pathway driven expression, the expression of mESC markers went down and mEpiLC markers went up comparably upon differentiation WT XX and XXTet3-/- mESCs, suggesting that many key transcriptional changes that characterize this transition can occur without TET3.

2022-09-01 | GSE171847 | GEO

ATAC-seq in TX1072 XXΔXic and XO mESCs during differentiation

Project description:ATAC-seq in TX1072 XXΔXic and XO mESCs during differentiation

| PRJNA704380 | ENA

STARR-seq in 1.8 XX and XO mESCs during differentiation

Project description:STARR-seq in 1.8 XX and XO mESCs during differentiation

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RRBS in XX and XO Xmas ES cells

Project description:This experiment is designed to test if our new culture protocol affects DNA methylation of XX mESCs

2022-10-31 | GSE160367 | GEO

RNAseq in Dppa2 knockout or wildtype TX1072 ESC during and after Xist over-expression

Project description:To understand the role of DPPA2 in epigenetic memory during X-Chromosome reactivation (XCR) we employed inducible Xist hybrid female embryonic stem cell line (TX1072, hybrid Bl6/Cast). Wild type or Dppa2 knockout TX1072 cells were cultured, in three or two independent biological replicates, respectively, in presence of DOX (1ug/ml) for 6 days to induce Xist overexpression and X-Chomosome inactivation (XCI) on the Bl6 allele. DOX was then washed out to silence Xist and XCR was followed in a time-series at 1, 3 or 7 days after DOX removal. Cell pellets were harvested at the following timepoints: -DOX, +DOX, 1d D-wo, 3d D-wo and 7d D-wo. RNA was extracted and 250 ng used for PolyA mRNA library preparation and Next generation sequencing.

2021-11-23 | E-MTAB-11183 | biostudies-arrayexpress

Non-coding CRISPR interference screen to identify regulatory elements of Xist in TX1072 XX SP107 mESCs at the onset of random X inactivation

Project description:Non-coding CRISPR interference screen to identify regulatory elements of Xist in TX1072 XX SP107 mESCs at the onset of random X inactivation

| PRJNA704374 | ENA

TT-seq and RNA-seq in TX1072 XXΔXic and XO mESCs during differentiation

Project description:TT-seq and RNA-seq in TX1072 XXΔXic and XO mESCs during differentiation

| PRJNA704378 | ENA