Transcriptomics profiling of human PSC cultured under different conditions

SND-ID: 2024-505. Version: 1. DOI: https://doi.org/10.48723/fr58-f782

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Associated documentation

README.txt (1.57 KB)

Sample table.csv (5.93 KB)

Citation

Creator/Principal investigator(s)

Anna Falk - Karolinska Institutet, Department of Neuroscience

Research principal

Karolinska Institutet - Department of Neuroscience

Description

This study has used transcriptome data derived for quality testing of pluripotent stem cells to investigate how different culture conditions affect gene expression. All pluripotent stem cells in the study have passed pluritest testing.
Data contains transcriptomics signatures of pluripotent stem cell lines originating from human donors, measured with Illumina Gene Expression HT12 Direct Hybridization assay (Illumina HT 12v.4). Human induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs) were cultured under either undefined culture conditions or defined and xenofree culture conditions, or transferred from the undefined to defined condition. These are labeled as feeder, laminin and transfer in the sample table, respectively. Skin biopsy samples were collected with informed consent from donors for creating models for studying human development. Donor samples were reprogrammed to iPSC and transcriptome analyses were performed for quality testing of the pluripotent cells.

The dataset consists of 115 files in IDAT format and one in CSV format.
The total size of the dataset is approx

Data contains personal data

Yes

Sensitive personal data

Yes

Type of personal data

Pseudo anonymized IDs of biological samples, sex

Code key exists

Yes

Language

English

Method and outcome

Population

Donors of skin cells come from cohorts of patients in neurology, ASD, rare diseases, neurodevelopmental disorders, and healthy donors. The cells used in the study come from donor material collected from 2012 onwards from cohorts of 100-400 individuals collected in Sweden. Skin biopsies are collected from donors after informed consent for research on modeling early human development.

Study design

Preclinical study

Description of study design

The purpose of the study was to see how much of the variation in gene expression can be explained by culture conditions, therefore comparisons have been made between as many cells as possible from different origins. The donor samples were reprogrammed into iPCS and transcriptome analyzes were performed to quality test the pluripotent stem cells. The establishment of iPSC has been done between 2012-2019.

Sampling procedure

Non-probability: Availability
Non-probability: Purposive

Not all donated cells were used for reprogramming because the process takes a long time and is very expensive. The selection of which donor cells were used for iPSC establishment was random and depended on available resources in terms of time and money. Data comes from men and women of different ages and this selection was also random and dependent on when we had resources. The data consists of 113 transcriptomes from 70 donors.

Data format / data structure

Numeric

Data collection

Geographic coverage

Administrative information

Responsible department/unit

Department of Neuroscience

Contributor(s)

Benjamin Ulfenborg - University of Skövde, School of Bioscience

Ilse Eidhof - Karolinska Institutet, Department of Medical Biochemistry and Biophysics

Funding 1

Funding agency: Swedish Research Council
Funding agency's reference number: 2017-03407
Project name on the application: Fate choices by neural stem cells and the effect on psychiatric disorders

Funding 2

Funding agency: Swedish Research Council
Funding agency's reference number: 2019-01498
Project name on the application: Fate choices by neural stem cells

Funding 3

Funding agency: Hjärnfonden
Funding agency's reference number: FO2019-0246
Project name on the application: Fate choice mechanisms by Neural Stem Cells causing Psychiatric Disorders

Ethics Review

Stockholm - Ref. 2012/208-31/3

Ethical approval for reprogramming of human cells where all samples have been taken from donors with approved informed consent.

Topic and keywords

Research area

Medical biotechnology (focus on cell biology (incl. stem cell biology), molecular biology, microbiology, biochemistry or biopharmacy) (Standard för svensk indelning av forskningsämnen 2011)

Keywords

Gene expression, Calcium signaling, Pluripotent stem cells, Cell culture, Stem cells, Gene expression, Pluripotent stem cells, Calcium signalling