Dataset features

Specifications


Application: DNA methylation array analysis
Number of samples: 9
Release date: Mar 14 2017
Last update date: Nov 27 2018
Access: Public
Computational protocol: limma, AgiMicroRna, IMA, GenomeTools, DAVID
Dataset link Time series DNA methylation analysis of immature T-cells and reMAIT cells by using methylation array

Experimental Protocol


MAITs isolated from CB were reprogrammed to iPSCs (PMID:23523177). The MAIT-derived iPSCs were cultured on OP9, and CD34+ CD43+ cells were isolated. These CD34+ CD43+ precursor cells were furthered cultured on OP9/DL1 for re-differentiation into MAITs. Based on the observation of the reported surface antigen profiles (PMID:23523177), reMAITs were harvested at four different time points: day 0 (Start), day 4 (Early), day 7-10 (Middle), and after day 30 (Late). For the immature T cells, CD34+ cells were isolated from CB using CD34 MicroBead Kit (Miltenyi Biotech). These CD34+ HSCs were cultured on OP9/DL1 for differentiation into T cell lineage as previously described (PMID:15494433). Based on the surface antigen profiles, the immature T cells were harvested at four different time points: CD34+ cells at day 0 (Start), CD4- CD8- double negative cells at day 21 (Early) and day 40 (Midlle), and CD4+ CD8+ double positive cells after day 50 (Late). For DNA methylation analysis, Genomic DNA was extracted from each sample using Wizard Genomic DNA Purification Kit (Promega, Tokyo, Japan). DNA (1 micro gram) was subjected to bisulfite conversion using EZ DNA Methylation Kit (Zymo Research, CA, USA), and subjected to analysis using Infinium HumanMethylation450 BeadChip Kit (Illumina, Tokyo, Japan).

Repositories


GEO

GSE88937

BioProject

PRJNA349150

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