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

Citation

Creator/Principal investigator(s)

Pedro Luis Moura - Karolinska Institutet, Department of Medicine, Huddinge / Center for Hematology and Regenerative Medicine (HERM) orcid

Eva Hellström-Lindberg - Karolinska Institutet, Department of Medicine, Huddinge / Center for Hematology and Regenerative Medicine (HERM) orcid

Research principal

Karolinska Institutet - Department of Medicine, Huddinge / Center for Hematology and Regenerative Medicine (HERM) rorId

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

... Show more..
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. 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

Method and outcome

Unit of analysis

Population

Patients with Myelodysplastic neoplasms with ring sideroblasts (MDS-RS) and healthy donors

Study design

Preclinical study

Sampling procedure

Probability: Simple random
Non-probability: Availability
Mixed probability and non-probability
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.

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

Data format / data structure

Data collection
Geographic coverage
Administrative information

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)

Funding 1

  • Funding agency: Swedish Cancer Society
  • Funding agency's reference number: 21 0340

Funding 2

  • Funding agency: Knut and Alice Wallenberg Foundation
  • Funding agency's reference number: 2017.0359

Funding 3

  • Funding agency: Swedish Cancer Society
  • Funding agency's reference number: 19 0200

Funding 4

  • Funding agency: Swedish Research Council
  • Funding agency's reference number: 211133

Ethics Review

Stockholm - Ref. 2017/1090-31/4

Topic and keywords

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)

Publications

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

If you have published anything based on these data, please notify us with a reference to your publication(s). If you are responsible for the catalogue entry, you can update the metadata/data description in DORIS.

Versions

Version 1. 2023-10-19

Version 1: 2023-10-19

DOI: https://doi.org/10.48723/41wa-yv42

Contact for questions about the data

Eva Hellström-Lindberg

eva.hellstrom-lindberg@ki.se

Published: 2023-10-19
Last updated: 2023-11-06