{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Tajda Klobučar"],"organism":["Mus musculus"],"software":["nf-core/rnaseq version 3.4 (https://nf-co.re/rnaseq/3.4)"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15428"],"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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - Naive mESC (nPSCs) were grown in 2i conditions (PMID: 18497825).","Sample Collection - For control and semi-extractability samples: naive pluripotent stem cells (nPSCs) 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.","Sequencing - The resulting cDNA libraries were sequenced as paired-end 150 bp reads on NovaSeq X Plus Series (PE150).","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).","Library Construction - Libraries for sequencing were prepared using CORALL Total RNA-Seq with RiboCop rRNA depletion version 2 (Lexogen) with 1000 ng DNase-treated RNA as input."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data 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.","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.","Sequence Alignment - For analysis only Read 1 was used. 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."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Tajda Klobučar","Ira Iosub","Miha Modic"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq for identifying semi-extractable and OOPS RNAs in naive mouse embryonic stem cells (second batch)","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.","dates":{"release":"2025-09-16T00:00:00Z","modification":"2025-09-16T01:02:19.35Z","creation":"2025-07-25T12:36:22.705Z"},"accession":"E-MTAB-15428","cross_references":{"ENA":["ERP177271"],"Biostudies":["E-MTAB-14762"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}