RNA sekvensering av benmärgsceller från MDS-RS patienter och friska donatorer Bulk RNA sequencing of bone marrow cells from MDS-RS patients and healthy donors 2023-120-1-1 https://doi.org/10.48723/41wa-yv42 Swedish National Data Service Svensk nationell datatjänst Landing page RNA sekvensering av benmärgsceller från MDS-RS patienter och friska donatorer Bulk RNA sequencing of bone marrow cells from MDS-RS patients and healthy donors 2023-120-1-1 https://doi.org/10.48723/41wa-yv42 10.1158/0008-5472.CAN-23-3038 Moura, Pedro Luis Moura, Pedro Luis Hellström-Lindberg, Eva Hellström-Lindberg, Eva 21 0340 21 0340 2017.0359 2017.0359 19 0200 19 0200 2021-01404_VR 2021-01404_VR Swedish National Data Service Svensk nationell datatjänst Landing page Myelodysplastic-Myeloproliferative Diseases Myelodysplastiska-myeloproliferativa syndrom 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 libraries were cleaned up using SPRI beads in 22% PEG8000 buffer and eluted in 12 µL H2O. The dataset consists of 2 folders: - Bulk_Main - Minibulk_Cycloheximide The folder Bulk_Main contains 67 GNU zipped fastq files, 1 tsv file, and 1 txt file. The folder Minibulk_Cycloheximide contains 2 GNU zipped fastq files, and 4 txt files. The documentation file File_list_BulkMinibulk.txt contains a full list of the files in the dataset. The total size of the dataset is approximately 360 GB. 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. CellsCells CellerCeller Patients with Myelodysplastic neoplasms with ring sideroblasts (MDS-RS) and healthy donors Patienter med myelodysplastisk syndrom med ringsideroblaster (MDS-RS) samt friska donatorer Numeric Other Bone marrow (BM) and/or peripheral blood (PB) samples were collected from 36 MDS-RS and 3 MDS non-RS patients evaluated at Karolinska University Hospital, Huddinge, Sweden. Diagnostic procedures were performed according to the European LeukemiaNet recommendation and WHO classification for myeloid neoplasms. As the specific purpose was to dissect the pathobiology of SF3B1-mutant MDS-RS, all MDS-RS patients belonged to the SF3B1α category in the IPSS-M risk classification. RS presence was quantified according to standard clinical practice. Additional samples were collected from a total of 40 healthy normal bone marrow (NBM) donors for control purposes. Please note that a deidentified donor and experiment index is provided in the companion publication for this dataset, including clinical and mutational status. All source material was provided with written informed consent for research use, given in accordance with the Declaration of Helsinki.Bone marrow (BM) and/or peripheral blood (PB) samples were collected from 36 MDS-RS and 3 MDS non-RS patients evaluated at Karolinska University Hospital, Huddinge, Sweden. Diagnostic procedures were performed according to the European LeukemiaNet recommendation and WHO classification for myeloid neoplasms. As the specific purpose was to dissect the pathobiology of SF3B1-mutant MDS-RS, all MDS-RS patients belonged to the SF3B1α category in the IPSS-M risk classification. RS presence was quantified according to standard clinical practice. Additional samples were collected from a total of 40 healthy normal bone marrow (NBM) donors for control purposes. Please note that a deidentified donor and experiment index is provided in the companion publication for this dataset, including clinical and mutational status. All source material was provided with written informed consent for research use, given in accordance with the Declaration of Helsinki. Probability: Simple randomProbability: Simple random Sannolikhetsurval: obundet slumpmässigt urvalSannolikhetsurval: obundet slumpmässigt urval Non-probability: AvailabilityNon-probability: Availability Icke-sannolikhetsurval: tillgänglighetsurvalIcke-sannolikhetsurval: tillgänglighetsurval Mixed probability and non-probabilityMixed probability and non-probability Blandat sannolikhets- och icke-sannolikhetsurvalBlandat sannolikhets- och icke-sannolikhetsurval Access to data through SND. Access to data is restricted. Åtkomst till data via SND. Tillgång till data är begränsad. restrictedAccess Moura PL, Mortera Blanco T, Hofman IJ, Todisco G, Kretzschmar WW, Björklund AC, Creignou M, Hagemann-Jensen M, Ziegenhain C, Cabrerizo Granados D, Barbosa I, Walldin G, Jansson M, Ashley N, Mead AJ, Lundin V, Dimitriou M, Yoshizato T, Woll PS, Ogawa S, Sandberg R, Jacobsen SW, Hellström-Lindberg E. Erythroid differentiation enhances RNA mis-splicing in SF3B1-mutant myelodysplastic syndromes with ring sideroblasts. Cancer Res. 2023 Nov 3. doi: 10.1158/0008-5472.CAN-23-3038. Moura PL, Mortera Blanco T, Hofman IJ, Todisco G, Kretzschmar WW, Björklund AC, Creignou M, Hagemann-Jensen M, Ziegenhain C, Cabrerizo Granados D, Barbosa I, Walldin G, Jansson M, Ashley N, Mead AJ, Lundin V, Dimitriou M, Yoshizato T, Woll PS, Ogawa S, Sandberg R, Jacobsen SW, Hellström-Lindberg E. Erythroid differentiation enhances RNA mis-splicing in SF3B1-mutant myelodysplastic syndromes with ring sideroblasts. Cancer Res. 2023 Nov 3. doi: 10.1158/0008-5472.CAN-23-3038. 10.1158/0008-5472.CAN-23-3038 2023