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T-cell differentiation


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Species:Mouse (Mus musculus)
Genomic View:Zenbu
Expression table:FILE
Link to TET:TET
Sample providers :Hiroshi Kawamoto
Germ layer:mesoderm
Primary cells or cell line:primary cells
Time span:6 days
Number of time points:15


T cells are produced in the thymus. The earliest T cell progenitors in the thymus are not fully committed to the T cell lineage but retain potentials to give rise to other lineage cells, myeloid cells, dendritic cells and natural killer cells. The T cell progenitors gradually lose their potential and commit to the T cell lineage through interacting with thymic epithelial cells. However, the exact mechanisms are still poorly understood. Especially, the transcriptional networks controlling the T cell fate determination remain elusive because of the lack of suitable experimental systems. Here, we have established a coculture system using EBF1KO hematopoietic progenitor cells (HPCs) with the TSt-4/Delta-like (DLL) 1 stromal cells that support the T cell differentiation[1,2]. By applying this time course samples to CAGE analysis, we examined the gene regulatory networks underlying the T cell lineage commitment from multipotent hematopoietic progenitors.

[1] Lin YC, Jhunjhunwala S, Benner C, Heinz S, Welinder E, Mansson R, Sigvardsson M, Hagman J, Espinoza CA, Dutkowski J, Ideker T, Glass CK, Murre C. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol. 11(7): 635-643, 2010
[2] Ikawa T, Hirose S, Masuda K, Kakugawa K, Satoh R, Shibano-Satoh A, Kominami R,Katsura Y, and Kawamoto H. An essential developmental checkpoint for production of the T cell lineage. Science 329: 93-96, 2010

Sample description

We used EBF1KO HPCs, which were isolated from day 15 fetal livers of EBF1KO mice[1]. EBF1KO HPCs were maintained on TSt-4 stromal cells in IMDM (SIGMA) supplemented with 10% FBS (Life Technologies), 2-ME (5 x 10-5 M; Nacalai tesque), streptomycin (100mg/ml), penicillin (100U/ml) (both from Life Technologies), SCF, IL-7 and Flt3-L (all from R&D). 1 x 106 EBF1KO cells were transferred to TSt-4/DLL1 cells to induce T lineage differentiation. T lineage commitment was verified by the surface expression of CD117 and CD25 at day 6 of the culture. After inducing T lineage differentiation, we harvested the samples at 0 h, 0.5 h, 1 h, 2 h, 4 h, 6 h, 8 h, 10 h, 12 h, 24 h, 48 h, 72 h, 96 h, 120 h, 144 h of the culture. The 0 h time point serves as a control for the other time points (Figure 1).

Figure 1: Schematic experimental procedure for the time course analysis. EBF1KO cells were transferred and cultured on the TSt-4/DLL1 stromal cells to induce T cell differentiation. The cells were harvested at each time point indicated in the figure. Total RNA was purified using miRNeasy Micro Kit (Qiagen) and served for CAGE analysis.

Quality control

Figure 2: CAGE expression of marker genes in TPM.

Profiled time course samples

Only samples that passed quality controls (Arner et al. 2015) are shown here. The entire set of samples are downloadable from FANTOM5 human / mouse samples

12971-138H1TSt-4/DLL1 feeder cells, biol_rep1{{{time}}}{{{donor}}}
12972-138H2EBF KO HPCs induced to T cell00hr00minbiol_rep1
12973-138H3EBF KO HPCs induced to T cell00hr30minbiol_rep1
12974-138H4EBF KO HPCs induced to T cell01hrbiol_rep1
12975-138H5EBF KO HPCs induced to T cell02hrbiol_rep1
12976-138H6EBF KO HPCs induced to T cell04hrbiol_rep1
12977-138H7EBF KO HPCs induced to T cell06hrbiol_rep1
12978-138H8EBF KO HPCs induced to T cell08hrbiol_rep1
12979-138H9EBF KO HPCs induced to T cell10hrbiol_rep1
12980-138I1EBF KO HPCs induced to T cell12hrbiol_rep1
12981-138I2EBF KO HPCs induced to T cell24hrbiol_rep1
12982-138I3EBF KO HPCs induced to T cellday02biol_rep1
12983-138I4EBF KO HPCs induced to T cellday03biol_rep1
12984-138I5EBF KO HPCs induced to T cellday04biol_rep1
12985-138I6EBF KO HPCs induced to T cellday05biol_rep1
12986-138I7EBF KO HPCs induced to T cellday06biol_rep1
12987-138I8TSt-4/DLL1 feeder cells, biol_rep2{{{time}}}{{{donor}}}
12988-138I9EBF KO HPCs induced to T cell00hr00minbiol_rep2
12989-139A1EBF KO HPCs induced to T cell00hr30minbiol_rep2
12990-139A2EBF KO HPCs induced to T cell01hrbiol_rep2
12991-139A3EBF KO HPCs induced to T cell, 02hr, biol_rep2{{{time}}}{{{donor}}}
12992-139A4EBF KO HPCs induced to T cell04hrbiol_rep2
12993-139A5EBF KO HPCs induced to T cell06hrbiol_rep2
12994-139A6EBF KO HPCs induced to T cell08hrbiol_rep2
12995-139A7EBF KO HPCs induced to T cell10hrbiol_rep2
12996-139A8EBF KO HPCs induced to T cell12hrbiol_rep2
12997-139A9EBF KO HPCs induced to T cell24hrbiol_rep2
12998-139B1EBF KO HPCs induced to T cellday02biol_rep2
12999-139B2EBF KO HPCs induced to T cellday03biol_rep2
13000-139B3EBF KO HPCs induced to T cellday04biol_rep2
13001-139B4EBF KO HPCs induced to T cellday05biol_rep2
13002-139B5EBF KO HPCs induced to T cellday06biol_rep2
13003-139B6TSt-4/DLL1 feeder cells, biol_rep3{{{time}}}{{{donor}}}
13004-139B7EBF KO HPCs induced to T cell00hr00minbiol_rep3
13005-139B8EBF KO HPCs induced to T cell00hr30minbiol_rep3
13006-139B9EBF KO HPCs induced to T cell01hrbiol_rep3
13007-139C1EBF KO HPCs induced to T cell02hrbiol_rep3
13008-139C2EBF KO HPCs induced to T cell04hrbiol_rep3
13009-139C3EBF KO HPCs induced to T cell06hrbiol_rep3
13010-139C4EBF KO HPCs induced to T cell08hrbiol_rep3
13011-139C5EBF KO HPCs induced to T cell10hrbiol_rep3
13012-139C6EBF KO HPCs induced to T cell12hrbiol_rep3
13013-139C7EBF KO HPCs induced to T cell, 24hr, biol_rep3{{{time}}}{{{donor}}}
13014-139C8EBF KO HPCs induced to T cellday02biol_rep3
13015-139C9EBF KO HPCs induced to T cellday03biol_rep3
13016-139D1EBF KO HPCs induced to T cellday04biol_rep3
13017-139D2EBF KO HPCs induced to T cellday05biol_rep3
13018-139D3EBF KO HPCs induced to T cell, day06, biol_rep3{{{time}}}{{{donor}}}