Bulk RNA sequencing of bone marrow cells from MDS-RS patients and healthy donors
type: Dataset
distribution: Landing page for the dataset
title: RNA sekvensering av benmärgsceller från MDS-RS patienter och friska donatorer @sv
description: This dataset consists of bulk RNA sequencing data of MACS-separated bone marrow cells (CD34+ stem cells, GPA+ erythroblasts, CD71+ reticulocytes, ring sideroblasts and siderocytes) obtained from multiple healthy bone marrow donors and MDS-RS patients. A second minibulk dataset is included, where CD34+ and GPA+ cells were treated with cycloheximide or left untreated. The objective of this data collection was to assess several parameters on how the bone marrow of MDS-RS patients differs from that of healthy donors. This dataset includes raw sequencing data in .fastq format, processed count matrices and associated pseudonymized metadata. Processing: Bulk: CD34+ HSPC samples, mixed GPA+ erythroblast samples and CD71+ PB reticulocyte samples (RetPB) were isolated through MACS. RS and siderocytes were obtained through MACS+FACS. 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. Minibulk: Minibulk RNAseq was performed for assessment of cycloheximide treatment effects in CD34+ and GPA+ cell populations. The library preparation procedure was performed using the Xpress Genomics bulk RNA-seq kit v1, automated on a SP960 liquid handler (MGI Tech). In short, the library preparation procedure denatures RNA samples in presence of oligo-dT primer, which is followed by reverse transcription of RNA with a template-switching procedure and pre-amplification of full-length cDNA for 10 PCR cycles. cDNA was subsequently tagmented using Tn5 (TDE1 Tagment DNA Enzyme; Illumina) and reactions quenched after 10 min at 55 °C by addition of 0.2 % SDS (Sigma-Aldrich). Tagmented DNA was indexed using custom dual-unique Nextera index primers in a 12 cycle PCR reaction. Indexed librar…
description: Syftet med denna datainsamling var att bedöma flera parametrar om hur benmärgen hos MDS-RS-patienter skiljer sig från den hos friska donatorer. Denna datauppsättning består av RNA sekvensering av benmärgsceller från MDS-RS patienter och friska donatorer. Se den engelska beskrivningen för mer information. Datasetet består av två mappar: - Bulk_Main - Minibulk_Cycloheximide Mappen Bulk_Main innehåller 67 GNU zippade fastq-filer, 1 tsv-fil och 1 txt-fil. Mappen Minibulk_Cycloheximide innehåller 2 GNU zippade fastq-filer och 4 txt-filer. Dokumentationsfilen File_list_BulkMinibulk.txt innehåller en lista över datasetets alla filer. Datasetets totala storlek är ungefär 360 GB. @sv
modified: 2026-03-19T12:06:57.680995Z
issued: 2023-10-19T13:51:02.786065Z
publisher: Karolinska Institutet
theme: HEAL
access rights: NON PUBLIC
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Pedro Luis Moura
    type: Agent
    account: https://orcid.org/0000-0002-0493-5394
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Eva Hellström-Lindberg
    type: Agent
    account: https://orcid.org/0000-0002-7839-3743
    type: PrivateIndividual(s)
contact point: Individual
  fn: Eva Hellström-Lindberg
keyword: Myelodysplastic-Myeloproliferative Diseases
keyword: Myelodysplastiska-myeloproliferativa syndrom @sv
keyword: mds-rs
keyword: myelodysplastic syndromes
keyword: myelodysplastiska syndrom @sv
keyword: sf3b1
language: ENG

Landing page for the dataset
type: Distribution
title: Landningssida för datasetet @sv
access URL: Bulk RNA sequencing of bone marrow cells from MDS-RS patients and healthy donors
availability: stable

Karolinska Institutet
type: Agent
type: Academia-ScientificOrganisation
source: https://ror.org/056d84691