TMT proteomics of erythroblasts from healthy donors and erythroblasts/ring sideroblasts from MDS-RS patients
SND-ID: 2023-118-1. Version: 1. DOI: https://doi.org/10.48723/f2xa-4005
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 semi-quantitative 10-plex TMT proteomics analysis of FACS-separated bone marrow cells obtained from 3 healthy bone marrow donors and 3 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. The samples included in this analyses were 3 samples of sorted GPA+ erythroblasts pooled from 5 healthy donors (2+2+1) and 3 samples of sorted GPA+ erythroblasts plus 3 samples of purified ring sideroblats from 3 MDS-RS patients.
This dataset includes the raw mass spectra, QC and processed results.
Processing: In short, FACS-separated samples were snap frozen in liquid nitrogen. Cell pellets were lysed with 4 % SDS lysis buffer and prepared for mass spectrometry using a modified version of the SP3 protein clean up and digestion protocol published by Moggridge S. et al 2018.
The following files are included in the dataset:
- Processed data and analysis.xlsx (2.63 MB)
- Variable_list_Processed_data_and_analysis.xlsx (23 KB)
This dataset includes the raw mass spectra, QC and processed results.
Processing: In short, FACS-separated samples were snap frozen in liquid nitrogen. Cell pellets were lysed with 4 % SDS lysis buffer and prepared for mass spectrometry using a modified version of the SP3 protein clean up and digestion protocol published by Moggridge S. et al 2018.
The following files are included in the dataset:
- Processed data and analysis.xlsx (2.63 MB)
- Variable_list_Processed_data_and_analysis.xlsx (23 KB)
- Readme for raw data .zip file.txt (562 bytes)
- Readme for Processed data.xlsx file (1.07 KB)
- 13553_STD_EAEHPM1_10_TMT10_HiRIEF_3-10pH_20210504_07.15.zip (7.68 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
In this dataset, samples from 3 MDS-RS patients and 3 healthy donors are included.
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)
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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