Bulk RNA sequencing of bone marrow cells from MDS-RS patients and healthy donors
SND-ID: 2023-120-1. Version: 1. DOI: https://doi.org/10.48723/41wa-yv42
Associated documentation
Citation
Creator/Principal investigator(s)
Pedro Luis Moura - Karolinska Institutet, Department of Medicine, Huddinge / Center for Hematology and Regenerative Medicine (HERM)
Eva Hellström-Lindberg - Karolinska Institutet, Department of Medicine, Huddinge / Center for Hematology and Regenerative Medicine (HERM)
Research principal
Karolinska Institutet - Department of Medicine, Huddinge / Center for Hematology and Regenerative Medicine (HERM)
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
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. Show less..
Data contains personal data
Yes
Sensitive personal data
Yes
Type of personal data
Genetic and biological data of patients
Code key exists
Yes
Language
Unit of analysis
Population
Patients with Myelodysplastic neoplasms with ring sideroblasts (MDS-RS) and healthy donors
Study design
Preclinical study
Sampling procedure
Non-probability: Availability
Mixed probability and non-probability
Biobank is connected to the study
This study has used existing samples from a scientific collection or biobank
Scientific collection or biobank name: Karolinska Institutet MDS biobank
Type(s) of sample: Bone marrow cells
Responsible department/unit
Department of Medicine, Huddinge / Center for Hematology and Regenerative Medicine (HERM)
Contributor(s)
Gabriele Todisco - Karolinska Institutet, Department of Medicine, Huddinge / Center for Hematology and Regenerative Medicine (HERM)
Ethics Review
Stockholm - Ref. 2017/1090-31/4
Research area
Natural sciences (Standard för svensk indelning av forskningsämnen 2011)
Biological sciences (Standard för svensk indelning av forskningsämnen 2011)
Cell biology (Standard för svensk indelning av forskningsämnen 2011)
Genetics (Standard för svensk indelning av forskningsämnen 2011)
Bioinformatics and systems biology (Standard för svensk indelning av forskningsämnen 2011)
Hematology (Standard för svensk indelning av forskningsämnen 2011)
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.
DOI:
https://doi.org/10.1158/0008-5472.CAN-23-3038
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