10X single-cell RNA sequencing of bone marrow cells from MDS-RS patients and healthy donors

SND-ID: 2023-121-1. Version: 1. DOI: https://doi.org/10.48723/nq2a-1e03

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 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 aga

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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. 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)

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)

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/nq2a-1e03

Contact for questions about the data

Eva Hellström-Lindberg

eva.hellstrom-lindberg@ki.se

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