RNA sekvensering av erytroblaster från inducerade pluripotenta stamcellslinjer (iPSC) med vildtyp och muterad SF3B1 Bulk RNA sequencing of erythroblasts from a pair of SF3B1-mutated and SF3B1-wildtype induced pluripotent stem cell (iPSC) lines 2024-128-1 https://doi.org/10.48723/3hs1-0v44 Swedish National Data Service Svensk nationell datatjänst Landing page RNA sekvensering av erytroblaster från inducerade pluripotenta stamcellslinjer (iPSC) med vildtyp och muterad SF3B1 Bulk RNA sequencing of erythroblasts from a pair of SF3B1-mutated and SF3B1-wildtype induced pluripotent stem cell (iPSC) lines 2024-128-1 https://doi.org/10.48723/3hs1-0v44 10.1038/s41375-025-02740-1 Thier, Jonas Thier, Jonas Hellström-Lindberg, Eva Hellström-Lindberg, Eva Moura, Pedro Moura, Pedro Lundin, Vanessa Lundin, Vanessa Swedish National Data Service Svensk nationell datatjänst Landing page Myelodysplastic Syndromes Myelodysplastiskt syndrom Myelodysplastic-Myeloproliferative Diseases Myelodysplastiska-myeloproliferativa syndrom Induced Pluripotent Stem Cells Inducerade pluripotenta stamceller 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. CellsCells CellerCeller Cell lines from a patient with SF3B1-mutant myelodysplastic neoplasm with ring sideroblasts (MDS-RS) Cellinjer från en patient med SF3B1-muterad myelodysplastisk neoplasi med ringsideroblaster (MDS-RS) Other Non-probability: AvailabilityNon-probability: Availability Icke-sannolikhetsurval: tillgänglighetsurvalIcke-sannolikhetsurval: tillgänglighetsurval Access to data through SND. Access to data is restricted. Åtkomst till data via SND. Tillgång till data är begränsad. restrictedAccess Thier, J., Hofmann, S., Kirchhof, K.M. et al. SF3B1-mutant models of RNA mis-splicing uncover UBA1 as a therapeutic target in myelodysplastic neoplasms. Leukemia (2025). https://doi.org/10.1038/s41375-025-02740-1 Thier, J., Hofmann, S., Kirchhof, K.M. et al. SF3B1-mutant models of RNA mis-splicing uncover UBA1 as a therapeutic target in myelodysplastic neoplasms. Leukemia (2025). https://doi.org/10.1038/s41375-025-02740-1 10.1038/s41375-025-02740-1 2025