10X singel-cell RNA sekvensering av benmärgsceller från MDS-RS patienter och friska donatorer 10X single-cell RNA sequencing of bone marrow cells from MDS-RS patients and healthy donors 2023-121-1-1 https://doi.org/10.48723/nq2a-1e03 Swedish National Data Service Svensk nationell datatjänst Landing page 10X singel-cell RNA sekvensering av benmärgsceller från MDS-RS patienter och friska donatorer 10X single-cell RNA sequencing of bone marrow cells from MDS-RS patients and healthy donors 2023-121-1-1 https://doi.org/10.48723/nq2a-1e03 10.1158/0008-5472.CAN-23-3038 Moura, Pedro Luis Moura, Pedro Luis Hellström-Lindberg, Eva Hellström-Lindberg, Eva 2017.0359 2017.0359 21 0340 21 0340 19 0200 19 0200 2021-01404_VR 2021-01404_VR Swedish National Data Service Svensk nationell datatjänst Landing page This dataset consists of single-cell RNA sequencing data of bone marrow cells (CD34+ stem cells, GPA+ erythroblasts, ring sideroblasts and mononuclear cells) obtained from multiple healthy bone marrow donors and MDS-RS patients. 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: All samples were loaded onto Chromium Single Cell Chips (10x Genomics, CA, USA) at a target capture rate of 10,000 cells per sample. Single cell libraries were prepared using Chromium Next GEM Single Cell 3ʹ Kits v3.1 (10x Genomics) as per the manufacturer’s instructions, except 1µl additive ADT primers were added to the initial cDNA PCR amplification buffer and ADT libraries prepared as described in the Total-Seq B protocol (BioLegend) from the initial cDNA SPRI clean up. Libraries were pooled and sequenced on an Illumina NovaSeq 6000 (Illumina). Read pseudoalignment was performed against the GRCh38.p13 human genome assembly through kallisto v0.46.1 and bustools v0.40.0 was used for barcode and UMI counting. The dataset consists of 2 folders: - Processed_Count_Matrices - Raw_FASTQ And one xlsx file: - Sample_key.xlsx The folder Processed_Count_Matrices contains 1 rds file, 1 tsv file, 9 mtx files, and 18 txt files. The folder Raw_FASTQ contains 27 GNU zipped fastq files, and 5 txt files. The documentation file File_list_10x.txt contains a full list of the files in the dataset. The total size of the dataset is approximately 21 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 singel-cell RNA sekvensering av benmärgsceller från MDS-RS patienter och friska donatorer. Se den engelska beskrivningen för mer information. Datasetet består av två mappar: - Processed_Count_Matrices - Raw_FASTQ och en xlsx-fil: - Sample_key.xlsx Mappen Processed_Count_Matrices innehåller 1 rds-fil, 1 tsv-fil, 9 mtx-filer och 18 txt-filer. Mappen Raw_FASTQ innehåller 27 GNU-zippade fastq-filer och 5 txt-filer. Dokumentationsfilen File_list_10x.txt innehåller en lista över datasetets alla filer. Datasetets totala storlek är ungefär 21 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