Smart-seq3 och Smart-seq3xpress singel-cell RNA sekvensering av benmärgsceller från MDS-RS patienter Smart-seq3 and Smart-seq3xpress single-cell RNA sequencing of bone marrow cells from MDS-RS patients 2023-122-1-1 https://doi.org/10.48723/0f0c-p816 Swedish National Data Service Svensk nationell datatjänst Landing page Smart-seq3 och Smart-seq3xpress singel-cell RNA sekvensering av benmärgsceller från MDS-RS patienter Smart-seq3 and Smart-seq3xpress single-cell RNA sequencing of bone marrow cells from MDS-RS patients 2023-122-1-1 https://doi.org/10.48723/0f0c-p816 10.1158/0008-5472.CAN-23-3038 Moura, Pedro Luis Moura, Pedro Luis Hellström-Lindberg, Eva Hellström-Lindberg, Eva 2017.0359 2017.0359 2021-01404_VR 2021-01404_VR 19 0200 19 0200 21 0340 21 0340 Swedish National Data Service Svensk nationell datatjänst Landing page Myelodysplastic Syndromes Myelodysplastiskt syndrom This dataset consists of Smart-seq3 single-cell RNA sequencing data of purified RS from the bone marrow and peripheral blood of 2 MDS-RS patients; and Smart-seq3xpress single-cell RNA sequencing data of FACS-sorted hematopoietic stem cells (HSC), multipotent progenitors (MPP), megakaryocyte-erythroid progenitors (MEP) and erythroblasts from 1 MDS-RS patient. 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: In brief, cells were sorted into 384-well plates containing 3uL Vapor-Lock (Qiagen) and 0.3uL lysis buffer consisting of 0.125 µM OligodT30VN (5'-Biotin-ACGAGCATCAGCAGCATACGAT30VN-3'; IDT) adjusted to reverse transcription (RT), 0.5mM dNTPs/each adjusted to RT volume, 0.1% Triton X-100, 5% PEG8000 adjusted to RT volume, 0.4u RNase Inhibitor (Takara Bio, 40 U/µL). After cell sorting plates were briefly centrifuged before storage at -80C. Before RT, plates were denatured at 72 degrees for 10 min followed by addition of 0.1 µL of RT mix; 25 mM Tris-HCL pH 8.4 (Fischer Scientific), 30mM NaCl (Ambion), 1 mM GTP (Thermo Fisher Scientific), 2.5 mM MgCl2 (Ambion), 8 mM DTT (Thermo Fisher Scientific), 0.25 U/µl RNase Inhibitor (Takara Bio), 0.75 µM Template Switching Oligo (TSO) (5′-Biotin-AGAGACAGATTGCGCAATGNNNNNNNNWWrGrGrG-3′; IDT) and 2 U/µl of Maxima H Minus reverse transcriptase (Thermo Fisher Scientific). Plates were quickly centrifuged after dispensing to ensure merge of lysis and RT volumes. RT was incubated at 42 °C for 90 minutes, followed by ten cycles of 50 °C for 2 minutes and 42 °C for 2 minutes. After RT, 0.6 µL PCR mix was dispensed to each well containing the following; 1× SeqAmp PCR buffer (Takara Bio), 0.025 U/µl of SeqAmp polymerase (Takara Bio) and 0.5 µM Smartseq3 forward and reverse primer. Plates were quickly spun down before being incubated as follows: 1 minute at 95 °C for initial denaturation, 14 cycles of 10 seconds at 98 °C, 30 seconds at 65 °C and 2–6 minutes at 68 °C. Final elongation was performed for 10 minutes at 72 °C. The dataset consists of 2 folders: - SS3_FACS_PB-BM_RS - SS3xpress_FACS_HSC_MPP_MEP_EB The folder SS3_FACS_PB-BM_RS contains 1 rds file, 3 txt files, and 1 compressed folder (tar.gz) with fastq files. The folder SS3xpress_FACS_HSC_MPP_MEP_EB contains 1 rds file, 7 txt files, and 2 GNU zipped fastq files. The documentation file File_list_SS3_SS3xpress.txt contains a full list of the files in the dataset. 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 Smart-seq3 och Smart-seq3xpress singel-cell RNA sekvensering av benmärgsceller från MDS-RS patienter. Se den engelska beskrivningen för mer information. Datasetet består av 2 mappar: - SS3_FACS_PB-BM_RS - SS3xpress_FACS_HSC_MPP_MEP_EB Mappen SS3_FACS_PB-BM_RS innehåller 1 rds-fil, 3 txt-filer och 1 komprimerad mapp (tar.gz) med fastq-filer. Mappen SS3xpress_FACS_HSC_MPP_MEP_EB innehåller 1 rds fil, 7 txt-filer och 2 GNU-zippade fastq-filer. Dokumentationsfilen File_list_SS3_SS3xpress.txt innehåller en lista över datasetets alla filer. CellsCells CellerCeller Patients with Myelodysplastic neoplasms with ring sideroblasts (MDS-RS) Patienter med myelodysplastisk syndrom med ringsideroblaster (MDS-RS) 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