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{{TimeCourse
{{TimeCourse
|TCOverview=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.<br><br>References: <br>[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<br>[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<br>
|TCQuality_control=<html><img src='https://fantom5-collaboration.gsc.riken.jp/resource_browser/images/TC_qc/1000px-Mouse_EBF_KO_HPCs_induced_to_T_cell.png' onclick='javascript:window.open("https://fantom5-collaboration.gsc.riken.jp/resource_browser/images/TC_qc/1000px-Mouse_EBF_KO_HPCs_induced_to_T_cell.png", "imgwindow", "width=1000,height=333");' style='width:700px;cursor:pointer'/></html><br>Figure 2: CAGE expression of marker genes in TPM.<br>
|TCSample_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).<br><html><img src='https://fantom5-collaboration.gsc.riken.jp/resource_browser/images/TC_qc/500px-T-cell_Fig1.png'></html><br>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.<br>
|Time_Course=
|Time_Course=
|category_treatment=differentiation
|collaborators=Hiroshi Kawamoto
|collaborators=Hiroshi Kawamoto
|description=mouse_EBF_KO_HPCs_induced_to_T_cell
|description=mouse_EBF_KO_HPCs_induced_to_T_cell
|germ_layer=mesoderm
|libraryids=CNhs11058,CNhs12231,CNhs12232,CNhs12233,CNhs12234,CNhs12235,CNhs12236,CNhs12237,CNhs12238,CNhs12239,CNhs12240,CNhs11059,CNhs12241,CNhs12242,CNhs11060,CNhs12980,CNhs12981,CNhs12982,CNhs12985,CNhs12986,CNhs12987,CNhs12988,CNhs12989,CNhs12990,CNhs12991,CNhs13684,CNhs13686,CNhs12992,CNhs12993,CNhs13687,CNhs13688,CNhs13689,CNhs13690,CNhs13691,CNhs13587,CNhs13588,CNhs13589,CNhs13590,CNhs13592,CNhs13593,CNhs13595,CNhs13596
|libraryids=CNhs11058,CNhs12231,CNhs12232,CNhs12233,CNhs12234,CNhs12235,CNhs12236,CNhs12237,CNhs12238,CNhs12239,CNhs12240,CNhs11059,CNhs12241,CNhs12242,CNhs11060,CNhs12980,CNhs12981,CNhs12982,CNhs12985,CNhs12986,CNhs12987,CNhs12988,CNhs12989,CNhs12990,CNhs12991,CNhs13684,CNhs13686,CNhs12992,CNhs12993,CNhs13687,CNhs13688,CNhs13689,CNhs13690,CNhs13691,CNhs13587,CNhs13588,CNhs13589,CNhs13590,CNhs13592,CNhs13593,CNhs13595,CNhs13596
|number_time_points=15
|page_name=mouse_T_cell
|page_name=mouse_T_cell
|primary_cells=primary cells
|series=IN_VITRO DIFFERENTIATION SERIES
|series=IN_VITRO DIFFERENTIATION SERIES
|species=Mouse (Mus musculus)
|species=Mouse (Mus musculus)
|tet_config=http://fantom.gsc.riken.jp/5/tet/search/?filename=mm9.cage_peak_phase1and2combined_tpm_ann_decoded.osc.txt.gz&file=1&c=1&c=33&c=34&c=35&c=36&c=37&c=38&c=39&c=40&c=42&c=41&c=44&c=45&c=46&c=47&c=48&c=49&c=50&c=51&c=52&c=53&c=54&c=55&c=56&c=57&c=58&c=59&c=60&c=61&c=63&c=64&c=65&c=66&c=67&c=68&c=69&c=70&c=71&c=72&c=73&c=74&c=75&c=76
|time_points=
|time_span=6 days
|timepoint_design=early focus
|tissue_cell_type=T-cells
|zenbu_config=http://fantom.gsc.riken.jp/zenbu/gLyphs/#config=SGBRasWzMlPrM-izUwsJCC
|zenbu_config=http://fantom.gsc.riken.jp/zenbu/gLyphs/#config=SGBRasWzMlPrM-izUwsJCC
|TCOverview=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.<br>
<br>
References: <br>
[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<br>
[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<br>
|TCSample_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).<br>
<html><img src='https://fantom5-collaboration.gsc.riken.jp/resource_browser/images/TC_qc/500px-T-cell_Fig1.png'></html><br>
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.<br>
|TCQuality_control=<html><img src='https://fantom5-collaboration.gsc.riken.jp/resource_browser/images/TC_qc/1000px-Mouse_EBF_KO_HPCs_induced_to_T_cell.png' onclick='javascript:window.open("https://fantom5-collaboration.gsc.riken.jp/resource_browser/images/TC_qc/1000px-Mouse_EBF_KO_HPCs_induced_to_T_cell.png", "imgwindow", "width=1000,height=333");' style='width:700px;cursor:pointer'/></html><br>
Figure 2: CAGE expression of marker genes in TPM.<br>
}}
}}

Revision as of 18:06, 3 February 2015

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


CollapseOverview

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.

References:
[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


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