10X single-cell RNA sequencing of hematopoietic stem and progenitor cells from a dual SF3B1-mutant MDS-RS patient and a healthy donor

SND-ID: 2023-222. Version: 1. DOI: https://doi.org/10.48723/tt0e-eq82

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Associated documentation

DualMT_10X_FileList.txt (780 bytes)

Readme_10X.txt (920 bytes)

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 10X single-cell RNA sequencing data of bone marrow cells (CD34+ stem cells) obtained from two clinical visits of a dual SF3B1-mutant MDS-RS patient (Patient 1 in the associated publication: visits at 31 months post-diagnosis, with dominant SF3B1 N626D; and at 118 months post-diagnosis, with dominant SF3B1 K666N) and one healthy bone marrow donor. The objective of this data collection was to assess how the hematopoietic stem and progenitor cell compartment of this patient differed over time and as a result of changes in clonal frequency.
The dataset is appoximately 80.9 GB and has filetypes txt, rds and fastq.

Data contains personal data

Yes

Sensitive personal data

Yes

Type of personal data

Genetic and biological data of patients

Code key exists

Yes

Language

English

Method and outcome

Unit of analysis

Cells

Population

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

Time Method

Time series: Discrete

Study design

Preclinical study

Sampling procedure

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

The data in this dataset comes from 1 dual SF3B1mt MDS-RS patient and 1 healthy donor. It is part of a study where bone marrow (BM) samples were collected from 2 dual SF3B1mt MDS-RS patients (Patient 1: N626D, K666N; Patient 2: K700E, K666N) evaluated at Karolinska University Hospital, Sweden. Diagnostic procedures were performed according to the European LeukemiaNet recommendation and WHO classification for myeloid neoplasms. Mutational status was evaluated at the clinic through panel sequencing for the most common myeloid mutations. Additional samples were collected from a total of 4 healthy NBM donors for control purposes. All source material was provided with written informed consent for research use, given in accordance with the Declaration of Helsinki, and the study was approved by the Ethics Research Committee at Karolinska Institutet.

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

Numeric

Other

Data collection

Geographic coverage

Administrative information

Responsible department/unit

Department of Medicine, Huddinge / Center for Hematology and Regenerative Medicine (HERM)

Funding 1

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

Funding 2

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

Funding 3

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

Funding 4

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

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)

Keywords

Mds-rs, Myelodysplastic syndromes, Sf3b1

Publications

Pedro Luis Moura, Yasuhito Nannya, Affaf Aliouat, Isabel Juliana Hofman, Teresa Mortera Blanco, Tetsuichi Yoshizato, Ryunosuke Saiki, Masahiro M Nakagawa, Maria Creignou, Ann-Charlotte Björklund, Gunilla Walldin, Indira Barbosa, Monika Jansson, Francesca Grasso, Edda M Elvarsdottir, Petter S Woll, Sten Eirik W Jacobsen, Seishi Ogawa, Eva Hellström-Lindberg, Competition of dual SF3B1mt clones in MDS-RS is associated with distinct RNA mis-splicing in hematopoietic stem cells,
Blood Neoplasia, 2024,100011, ISSN 2950-3280,
https://doi.org/10.1016/j.bneo.2024.100011.
DOI: https://doi.org/10.1016/j.bneo.2024.100011

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