T-cell differentiation: Difference between revisions
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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> | |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=' | |TCQuality_control=<html><img src='/resource_browser/images/TC_qc/1000px-Mouse_EBF_KO_HPCs_induced_to_T_cell.png' onclick='javascript:window.open("/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=' | |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='/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 | |category_treatment=Differentiation | ||
| Line 14: | Line 14: | ||
|series=IN_VITRO DIFFERENTIATION SERIES | |series=IN_VITRO DIFFERENTIATION SERIES | ||
|species=Mouse (Mus musculus) | |species=Mouse (Mus musculus) | ||
|tet_config= | |tet_config=https://fantom.gsc.riken.jp/5/suppl/tet/T_cell.tsv.gz | ||
|tet_file= | |tet_file=https://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_points= | ||
|time_span=6 days | |time_span=6 days | ||
|timepoint_design=Early focus | |timepoint_design=Early focus | ||
|tissue_cell_type=T-cells | |tissue_cell_type=T-cells | ||
|zenbu_config= | |zenbu_config=https://fantom.gsc.riken.jp/zenbu/gLyphs/#config=hOwWNWTrGFop_FGIa8WFhB | ||
}} | }} | ||
Latest revision as of 17:41, 14 March 2022
| Series: | IN_VITRO DIFFERENTIATION SERIES |
|---|---|
| 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 |
| Overview |
|---|
|
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. |
| 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). |
| Quality control |
|---|
|
|
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
| 12971-138H1 | TSt-4/DLL1 feeder cells, biol_rep1 | {{{time}}} | {{{donor}}} |
| 12972-138H2 | EBF KO HPCs induced to T cell | 00hr00min | biol_rep1 |
| 12973-138H3 | EBF KO HPCs induced to T cell | 00hr30min | biol_rep1 |
| 12974-138H4 | EBF KO HPCs induced to T cell | 01hr | biol_rep1 |
| 12975-138H5 | EBF KO HPCs induced to T cell | 02hr | biol_rep1 |
| 12976-138H6 | EBF KO HPCs induced to T cell | 04hr | biol_rep1 |
| 12977-138H7 | EBF KO HPCs induced to T cell | 06hr | biol_rep1 |
| 12978-138H8 | EBF KO HPCs induced to T cell | 08hr | biol_rep1 |
| 12979-138H9 | EBF KO HPCs induced to T cell | 10hr | biol_rep1 |
| 12980-138I1 | EBF KO HPCs induced to T cell | 12hr | biol_rep1 |
| 12981-138I2 | EBF KO HPCs induced to T cell | 24hr | biol_rep1 |
| 12982-138I3 | EBF KO HPCs induced to T cell | day02 | biol_rep1 |
| 12983-138I4 | EBF KO HPCs induced to T cell | day03 | biol_rep1 |
| 12984-138I5 | EBF KO HPCs induced to T cell | day04 | biol_rep1 |
| 12985-138I6 | EBF KO HPCs induced to T cell | day05 | biol_rep1 |
| 12986-138I7 | EBF KO HPCs induced to T cell | day06 | biol_rep1 |
| 12987-138I8 | TSt-4/DLL1 feeder cells, biol_rep2 | {{{time}}} | {{{donor}}} |
| 12988-138I9 | EBF KO HPCs induced to T cell | 00hr00min | biol_rep2 |
| 12989-139A1 | EBF KO HPCs induced to T cell | 00hr30min | biol_rep2 |
| 12990-139A2 | EBF KO HPCs induced to T cell | 01hr | biol_rep2 |
| 12991-139A3 | EBF KO HPCs induced to T cell, 02hr, biol_rep2 | {{{time}}} | {{{donor}}} |
| 12992-139A4 | EBF KO HPCs induced to T cell | 04hr | biol_rep2 |
| 12993-139A5 | EBF KO HPCs induced to T cell | 06hr | biol_rep2 |
| 12994-139A6 | EBF KO HPCs induced to T cell | 08hr | biol_rep2 |
| 12995-139A7 | EBF KO HPCs induced to T cell | 10hr | biol_rep2 |
| 12996-139A8 | EBF KO HPCs induced to T cell | 12hr | biol_rep2 |
| 12997-139A9 | EBF KO HPCs induced to T cell | 24hr | biol_rep2 |
| 12998-139B1 | EBF KO HPCs induced to T cell | day02 | biol_rep2 |
| 12999-139B2 | EBF KO HPCs induced to T cell | day03 | biol_rep2 |
| 13000-139B3 | EBF KO HPCs induced to T cell | day04 | biol_rep2 |
| 13001-139B4 | EBF KO HPCs induced to T cell | day05 | biol_rep2 |
| 13002-139B5 | EBF KO HPCs induced to T cell | day06 | biol_rep2 |
| 13003-139B6 | TSt-4/DLL1 feeder cells, biol_rep3 | {{{time}}} | {{{donor}}} |
| 13004-139B7 | EBF KO HPCs induced to T cell | 00hr00min | biol_rep3 |
| 13005-139B8 | EBF KO HPCs induced to T cell | 00hr30min | biol_rep3 |
| 13006-139B9 | EBF KO HPCs induced to T cell | 01hr | biol_rep3 |
| 13007-139C1 | EBF KO HPCs induced to T cell | 02hr | biol_rep3 |
| 13008-139C2 | EBF KO HPCs induced to T cell | 04hr | biol_rep3 |
| 13009-139C3 | EBF KO HPCs induced to T cell | 06hr | biol_rep3 |
| 13010-139C4 | EBF KO HPCs induced to T cell | 08hr | biol_rep3 |
| 13011-139C5 | EBF KO HPCs induced to T cell | 10hr | biol_rep3 |
| 13012-139C6 | EBF KO HPCs induced to T cell | 12hr | biol_rep3 |
| 13013-139C7 | EBF KO HPCs induced to T cell, 24hr, biol_rep3 | {{{time}}} | {{{donor}}} |
| 13014-139C8 | EBF KO HPCs induced to T cell | day02 | biol_rep3 |
| 13015-139C9 | EBF KO HPCs induced to T cell | day03 | biol_rep3 |
| 13016-139D1 | EBF KO HPCs induced to T cell | day04 | biol_rep3 |
| 13017-139D2 | EBF KO HPCs induced to T cell | day05 | biol_rep3 |
| 13018-139D3 | EBF KO HPCs induced to T cell, day06, biol_rep3 | {{{time}}} | {{{donor}}} |
