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A landscape of X-inactivation during human T-cell development in the thymus

https://doi.org/10.5878/ayae-p143
The aim of the study was to investigate X-inactivation during human T-cell development in the thymus. Thymocytes from six different developmental stages from nine individuals were isolated and studied regarding gene expression. The data set contains data from RNA sequencing, DNA methylation and whole exome sequencing. The dataset contains data from the manuscript "A landscape of X-inactivation during human T-cell development in the thymus" by Gylemo et al, and consists of results from RNA sequencing (fastq.gz), analysis of DNA methylation (Grn.idat), Smart-seq2 single-cell RNA sequencing (fastq.gz) and whole exome DNA sequencing (fastq.gz) of six developmental stages of thymocytes from nine individuals. The data is described on individual and cell-type level in the tab-separated metadata files (.tsv). MD5 checksums for each file are included.
Download documentation (6 files / 187.79 KiB)

Documentation files

  • EPIC_methylation_meta.tsv
    2.66 KiB
  • md5sums-2022-112-v2.txt
    101.05 KiB
  • Patient characteristics meta.tsv
    580 Bytes
  • RNaseq_bulk_meta.tsv
    6.32 KiB
  • RNAseq_smartseq2_meta.tsv
    76.61 KiB
  • WES_meta.tsv
    592 Bytes

Citation and access

Data access level:

Creator/​Principal investigator(s):

Research principal:

Data contains personal data:

Yes

Type of personal data:

Human data. The data is pseudonymized and contains ID-numbers that can be coupled to individuals through a code key.

Code key exists:

Yes

Sensitive personal data:

Yes

Citation:

Language:

Method and outcome

Unit of analysis:

Population:

Isolated thymocytes from nine persons were studied, four boys and five girls, all under 3 years that underwent cardiac surgery for correction of congenital heart defects.

Study design:

  • Experimental study

Sampling procedure:

Number of individuals/​objects:

9

Data format/​data structure:

Samples/material Collected from scientific collection/biobank

Name:

Biobank Väst 890

Type(s) of sample:

Isolerade thymocyter

Samples/material Existing from scientific collection/biobank

Name:

Geographic coverage

Geographic location:

Administrative information

Responsible department/​unit:

Institute of Clinical Sciences

Other research principals:

Contributor(s):

Ethics Review:

Gothenburg - 217-12

Project title: Studies of central tolerance induction in human thymus

Funding

Funding agency:

Award number:

2018-02752

Award title:

Clinical and experimental studies of tolerance mechanisms in the thymus aiming at the development of therapeutic targeting of the thymus in the treatment of autoimmune diseases

Funding agency:

Award number:

ALFGBG-965795

Award title:

Kliniska och experimentella studier av toleransmekanismer i thymus

Topic and keywords

Standard för svensk indelning av forskningsämnen 2025:

Keywords:

Relations

Homepage:

Publications

Citation:

Björn Gylemo, Maike Bensberg, Viktoria Hennings, Christina Lundqvist, , Alessandro Camponeschi, Dora Goldman, Aida Selimović, Antonio Lentini, Olov Ekwall, Colm E. Nestor (2024). A landscape of X-inactivation during human T-cell development [manuscript, resubmitted after revision].

Metadata

Versions

Version:

2

DOI:

https://doi.org/10.5878/ayae-p143Opens in a new tab

  • Data added:

    Since extended analyses were requested by reviewers we hade added two patient samples in this version 2. We have also extended the methodology by performing single-cell RNA sequencing on one if the patient samples.

Published:

Version:

1

DOI:

https://doi.org/10.5878/frw5-wd59Opens in a new tab

Published:

doris
gu_en
Published: