2026-10-12 https://api.researchdata.se/oai-pmh

oai:researchdata.se:2024-128/1 2026-03-05 subject:ssif:10604 subject:ssif:10609 subject:ssif:10610 subject:ssif:30202 subject:ssif:30203 subject:ssif:106 subject:ssif:302 subject:ssif:1 subject:ssif:3 principal:slug:karolinska-institutet

info:eu-repo/semantics/other http://purl.org/dc/dcmitype/Dataset https://doi.org/10.48723/3hs1-0v44 Bulk RNA sequencing of erythroblasts from a pair of SF3B1-mutated and SF3B1-wildtype induced pluripotent stem cell (iPSC) lines RNA sekvensering av erytroblaster från inducerade pluripotenta stamcellslinjer (iPSC) med vildtyp och muterad SF3B1 https://orcid.org/0009-0007-5226-0372 https://orcid.org/0000-0002-7839-3743 https://orcid.org/0000-0002-0493-5394 https://orcid.org/0000-0003-2335-3370 Cell Biology Cellbiologi Genetics and Genomics Genetik och genomik Bioinformatics and Computational Biology Bioinformatik och beräkningsbiologi Hematology Hematologi Cancer and Oncology Cancer och onkologi This dataset consists of bulk RNA sequencing data of MACS-separated GPA+ erythroblasts obtained from a pair of induced pluripotent stem cell (iPSC) lines with and without SF3B1-mutation, generated from an MDS patient (Asimomitis G et al. 2022, Blood Advances). The objective of this data collection was to assess how SF3B1 mutation changes the molecular profile of RNA splicing in erythropoiesis. This dataset includes minimally processed, visualisation-ready .bam format sequencing data for both of the lines. Processing: MDS patient iPSC line-derived hematopoietic stem and progenitor cells (HSPC) were cultured for 14 days in erythroid specification media (StemPro-34 SFM [Gibco] + 1% Pen/Strep [Cytiva], 2 mM L-glutamine [Sigma-Aldrich], 3.5 µM 1-Thioglycerol [Sigma-Aldrich], 1% Bovine Albumin Fraction V [Gibco], 150 µg/mL holo-transferrin [Sigma-Aldrich], 2 U/mL erythropoietin [Pfizer], 50 ng/mL Stem Cell Factor [PeproTech] and 50 ng/mL interleukin-3 [PeproTech]). At Day 14 of culture, mixed glycophorin A-positive (GPA+) erythroblast samples were isolated through MACS. Cells were lysed in RLT (Qiagen) + 40 mM dithiothreitol (Sigma-Aldrich) and RNA extraction was performed with RNeasy Micro Kit (Qiagen) with RNase-free DNase treatment according to the manufacturer’s protocol. RNA integrity numbers (RIN) were estimated using Agilent RNA 6000 Pico Kits (Agilent Technologies, CA, USA). A minimum RIN value of 6.5 was considered adequate. RNA sequencing (RNAseq) libraries were prepared from total RNA using SMARTer Stranded Total RNA-Seq Kits v2 - Pico Input Mammalian (Takara Bio, Japan), including enzymatic ribosomal depletion steps. Libraries were sequenced using an Illumina Novaseq 6000 S4 (Illumina, CA, USA) with paired-end 150bp configuration. Reads were pre-processed with TrimGalore v. 0.6.7 using CutAdapt v. 3.5 and BAM files were generated through via two-pass alignment with STAR v. 2.7.9a against the GRCh38.p13 human genome assembly. The dataset consists of 13 files: - 2 .bam files, one for the SF3B1-mutant sample and one for the wildtype sample; - 2. bai bam index files, one for each sample to facilitate analysis of the .bam files. - 8 .fastq raw data files, corresponding to a paired-end run of the two samples in two different lanes (2 x 2 x 2). - 1 gene-collapsed read count matrix (.txt) summarising read counts for both samples. The documentation file iPSCEB_FileList.txt contains a full list of the files in the dataset. The total size of the dataset is approximately 80 GB. Syftet med denna datainsamling var att bedöma hur SF3B1-mutation förändrar den molekylära profilen för RNA-splitsning vid erytropoes. Denna datauppsättning består av RNA sekvensering av erytroblaster från ett par av SF3B1-muterade och SF3B1-vildtyp inducerade pluripotenta stamcell (iPSC). Se den engelska beskrivningen för mer information. info:eu-repo/semantics/restrictedAccess https://creativecommons.org/licenses/by-nc-nd/4.0/ Karolinska Institutet Karolinska Institutet 2025-08-12T10:20:35.213602Z eng