biostudies-arrayexpressTajda KlobučarMus musculusnf-core/rnaseq version 3.4 (https://nf-co.re/rnaseq/3.4)https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14762Total 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.biostudies-arrayexpressSequencing - The resulting cDNA libraries were sequenced as single-end 100 bp reads on HiSeq.Growth Protocol - Naive mESC (nPSCs) were grown in 2i conditions (PMID: 18497825), primed (pPSCs) in N2B27 basal medium supplemented with ActA 20 ng/ml, bFGF 12 ng/mL, IWP2 2 µM, and dPSCs were acquired from pPSCs, by switching the medium to N2B27 basal medium supplemented with ActA 20 ng/mL, bFGF 12 ng/mL, Wnt3a 250 ng/mL for 24 hours before collecting them.Library Construction - Libraries for sequencing were prepared using CORALL Total RNA-Seq with RiboCop rRNA depletion verion 1 (Lexogen) with 500 ng DNase-treated RNA as input.Sample Collection - For control and semi-extractability samples: naive pluripotent stem cells (nPSCs), primed (pPSCs) and 1-day Wnt-differentiated cells (dPSC) were washed twice with PBS, then lysed by adding TRIzol to the plate and scraping the cells off. The samples were snap frozen on dry ice and stored at -80°C prior isolation. For OOPS, one confluent 10 cm plate was used per replicate, washed twice with ice-cold PBS before crosslinking them at 400 mJ/cm2 (UV 254 nm). After removing residual PBS, 1 mL TRIzol-LS was added to the plate before scraping off the cells content and transferring it to a 1.5 mL Eppendorf tube that was stored at -80°C.Nucleic Acid Extraction - For control: TRIzol samples were thawed and RNA was extracted from the aqueous phase, following manufacturer's instructions. For semi: TRIzol samples were thawed and heated for 10 min at 55°C and also passed 40 times through a 20G needle (PMID: 28404604). For OOPS: RNA was isolated from the interphase following published protocol (PMID: 30607034, PMID: 32651564).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - The nf-core/rnaseq version 3.4 pipeline generates a gene-level count matrix (\\"salmon.merged.gene_counts_length_scaled.tsv\\") from Salmon quantification, containing counts for all samples (used for differential expression analysis). The processed file provided here includes the counts from this matrix corresponding to the specified sample.Sequence Alignment - Raw FASTQ files were processed using nf-core/rnaseq version 3.4, with UMI-tools - UMI-based deduplication enabled using the UMI pattern 'NNNNNNNNNNNN', and with alignment using STAR, and read quantification using Salmon (--aligner star_salmon). For read alignment, the mouse reference genome (GRCm39, GENCODE release M27) was used.Data Transformation - The nf-core/rnaseq version 3.4 pipeline generates a gene-level TPM matrix (\\"salmon.merged.gene_tpm.tsv\\") from Salmon quantification, containing TPM values for all samples. The processed file provided here includes the TPM values from this matrix corresponding to the specified sample.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 4000RNA-seq of total RNAMus musculusTajda KlobučarIra IosubMiha ModicfalseRNA-seq for identifying semi-extractable and OOPS RNAs in naive and primed mouse embryonic stem cellsTotal 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 1.2025-09-16T00:00:00Z2025-09-16T01:02:21.841Z2025-01-20T22:22:44.491ZE-MTAB-14762ERP168500EFO_0002944EFO_0004170EFO_0009653EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0004184