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RNA-seq for identifying semi-extractable and OOPS RNAs in naive and primed mouse embryonic stem cells

ABSTRACT: RNA-seq for identifying semi-extractable and OOPS RNAs in naive and primed mouse embryonic stem cells

PROVIDER: PRJEB85069 | ENA |

REPOSITORIES: ENA

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RNA-seq for identifying semi-extractable and OOPS RNAs in naive and primed mouse embryonic stem cells

Project description:Total RNA-seq data from samples produced using conventional TRIzol RNA extraction (control), using the semi-extractability assay (PMID: 28404604) or Orthogonal Organic Phase Separation (OOPS; PMID: 30607034, PMID: 32651564) in naive mESCs (nPSCs), primed pluripotent stem cells (pPSCs) and 1-day Wnt-differentiated cells (dPSCs). Control samples RNA was extracted from the aqueous phase of non-heated and non-sheared TRIzol samples. The semi-extractability assay samples were prepared by heating and needle-shearing TRIzol samples prior to extraction. For OOPS, the RNA was extracted from the TRIzol interphase of UV-crosslinked cells (254 nm, 400 mJ/cm2). Total RNA-seq libraries were prepared using the CORALL Total RNA-Seq Kit with RiboCop (Single Indexing) - version 1.

2025-09-16 | E-MTAB-14762 | biostudies-arrayexpress

RNA-seq for identifying semi-extractable and OOPS RNAs in naive mouse embryonic stem cells (second batch)

Project description:RNA-seq for identifying semi-extractable and OOPS RNAs in naive mouse embryonic stem cells (second batch)

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SERIPH: A Two-Step Extraction Protocol for Selective Enrichment of Semi-Extractable RNAs

Project description:Conventional RNA extraction with acid guanidinium thiocyanate–phenol–chloroform (AGPC) reagents incompletely recovers a subset of transcripts, termed semi-extractable RNAs (seRNAs). This underrepresented RNA population includes architectural RNAs (arcRNAs), which scaffold membraneless organelles, as well as stress-induced downstream-of-gene readthrough transcripts (DoGs). Although our previously developed “improved” AGPC protocol incorporating physical disruption enhances seRNA recovery, it also co-extracts abundant, readily extractable RNAs, yielding mixed populations that hinder precise characterization of seRNAs. Here, we present SERIPH (Semi-Extractable RNA Isolation from the InterPHase), a simple two-step protocol that selectively enriches seRNAs by separating them from readily extractable RNA species. By depleting abundant extractable RNAs, SERIPH increases detection sensitivity, enabling the capture of weakly semi-extractable transcripts, including those of low abundance, that were overlooked by previous approaches. This increased sensitivity expands the detectable seRNA repertoire and reveals a broader genomic extent of DoG transcription than previously appreciated. Together, SERIPH provides a robust framework for high-resolution analysis of seRNA populations, advancing studies of RNA processing, transcriptional regulation, and RNA-mediated nuclear organization in stress responses and disease

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RNA-seq for identifying semi-extractable and OOPS RNAs in naive mouse embryonic stem cells after thapsigargin stress

Project description:RNA-seq for identifying semi-extractable and OOPS RNAs in naive mouse embryonic stem cells after thapsigargin stress

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RNA-seq for identifying semi-extractable and OOPS RNAs in naive mouse embryonic stem cells (second batch)

Project description:Total RNA-seq data from samples produced using conventional TRIzol RNA extraction (control), using the semi-extractability assay (PMID: 28404604) or Orthogonal Organic Phase Separation (OOPS; PMID: 30607034, PMID: 32651564) in naive mESCs (nPSCs). Control samples RNA was extracted from the aqueous phase of non-heated and non-sheared TRIzol samples. The semi-extractability assay samples were prepared by heating and needle-shearing TRIzol samples prior to extraction. For OOPS, the RNA was extracted from the TRIzol interphase of UV-crosslinked cells (254 nm, 400 mJ/cm2). Total RNA-seq libraries were prepared using the CORALL Total RNA-Seq Kit with RiboCop (Dual Indexing, UDI12A) - version 2.

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RNA-seq for identifying semi-extractable and OOPS RNAs in naive mouse embryonic stem cells after thapsigargin stress

Project description:Total RNA-seq data from samples produced using conventional TRIzol RNA extraction (control), using the semi-extractability assay (PMID: 28404604) or Orthogonal Organic Phase Separation (OOPS; PMID: 30607034, PMID: 32651564) in naive mESCs (nPSCs) after the cells were exposed to 10 μM thapsigargin for 30 minutes. Control samples RNA was extracted from the aqueous phase of non-heated and non-sheared TRIzol samples. The semi-extractability assay samples were prepared by heating and needle-shearing TRIzol samples prior to extraction. For OOPS, the RNA was extracted from the TRIzol interphase of UV-crosslinked cells (254 nm, 400 mJ/cm2). Total RNA-seq libraries were prepared using the CORALL Total RNA-Seq Kit with RiboCop (Dual Indexing, UDI12A) - version 2.

2026-08-17 | E-MTAB-17443 | biostudies-arrayexpress

SERIPH: A Two-Step Extraction Protocol for Selective Enrichment of Semi-Extractable RNAs

Project description:SERIPH: A Two-Step Extraction Protocol for Selective Enrichment of Semi-Extractable RNAs

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RNA-seq of naive and primed ES cells

Project description:Here we propose a set of molecular criteria for evaluating the naive human pluripotent state. We show by RNA-seq that transcription of transposable elements provides a sensitive measure of the concordance between pluripotent stem cells and early human development. RNA-seq of 4 naive ES samples in 4i/LA, 3 naive ES samples in 5i/LA, 2 transgene-dependant naive ES cell samples, and 5 primed ES cell samples (in hESM)

2016-07-15 | E-GEOD-83765 | biostudies-arrayexpress

Profiling human naive and primed pluripotent states

Project description:Here we analyse transcriptome profiles of naive, primed and intermediate populations of human pluripotent stem cells

2017-03-23 | GSE93241 | GEO

Cell-surface proteomics identifies differences in signalling and adhesion protein expression between naive and primed human pluripotent stem cells

Project description:Naive and primed human pluripotent stem cells (hPSC) provide valuable models to study cellular and molecular developmental processes. The lack of detailed information about cell-surface protein expression in these two pluripotent cell types prevents an understanding of how the cells communicate and interact with their microenvironments. Here, we used plasma membrane profiling to directly measure cell-surface protein expression in naive and primed hPSC. This unbiased approach quantified over 1700 plasma membrane proteins including those involved in cell adhesion, signalling and cell interactions. Notably, multiple cytokine receptors upstream of JAK-STAT signalling were more abundant in naive hPSC. In addition, functional experiments showed that FOLR1 and SUSD2 proteins are highly expressed at the cell surface in naive hPSC but are not required to establish human naive pluripotency. This study provides a comprehensive stem cell proteomic resource that uncovers differences in signalling pathway activity and has identified new markers to define human pluripotent states.

2020-04-17 | PXD015359 | Pride

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