|
| Status |
Public on Dec 31, 2017 |
| Title |
CD8 T cell phenotype following antigen education by lymphatic endothelial cells versus mature dendritic cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The goal of this study is to analyze differences in gene expression of CD8 T cells that are antigen-educated by lymphatic stromal cells versus traditional antigen-presenting cells. Naive antigen-specific CD8 T cells reactive against the model antigen ovalbumin (OVA) were isolated from spleens of OT-I transgenic mice. They were then co-cultured with OVA-pulsed mature dendritic cells (mDCs) versus lymphatic endothelial cells (LECs) for up to 3d. Each day, OT-I cells were isolated and prepared for RNAseq analysis to determine differences in gene expression as a function of antigen-presenting cell. Naive, LEC-educated, or DC-educated OT-I transcriptomes are provided here.
Grant ID - AdG-323053
Agency - European Research Council (ERC)
Grant Title - LYMPHIMMUNE - Flow in the tumor microenvironment: Linking mechanobiology with immunology
Grant ID - R01CA219304
Agency - US National Institutes of Health (NIH)
Grant Title - Paradoxical roles of tumor lymphangiogenesis on tumor immunity and implications for immunotherapy
|
| |
|
| Overall design |
lymphatic endothelial cells versus mature dendritic cells
|
| |
|
| Contributor(s) |
Vokali E, Yu SS, Swartz MA |
| Citation(s) |
31988323 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 CA219304 |
Paradoxical roles of tumor lymphangiogenesis on tumor immunity and implications for immunotherapy - Resubmission 01 |
UNIVERSITY OF CHICAGO |
Melody Ann Swartz |
|
| BioProject |
PRJNA347820 |
| Submission date |
Oct 17, 2016 |
| Last update date |
Jan 29, 2020 |
| Contact name |
Shann S Yu |
| E-mail(s) |
shannyu@uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
PME-Immunoengineering Center
|
| Street address |
5640 S Ellis Ave, Eckhardt Research Center
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (21)
|
|
| Relations |
| SRA |
SRP091421 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE88830_PRJNA347820_Genes_Counts_RPKMs.xls.gz |
16.0 Mb |
(ftp)(http) |
XLS |
| GSE88830_PRJNA347820_Transcripts_Counts_RPKMs.xls.gz |
19.5 Mb |
(ftp)(http) |
XLS |
| GSE88830_genes_differential_DC_d1-DC_d2.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_DC_d1-DC_d3.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_DC_d2-DC_d3.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_LEC_d1-DC_d1.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_LEC_d1-DC_d2.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_LEC_d1-DC_d3.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_LEC_d1-LEC_d2.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_LEC_d1-LEC_d3.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_LEC_d2-DC_d1.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_LEC_d2-DC_d2.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_LEC_d2-DC_d3.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_LEC_d2-LEC_d3.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_LEC_d3-DC_d1.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_LEC_d3-DC_d2.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_LEC_d3-DC_d3.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_Naive_1-DC_d1.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_Naive_1-DC_d2.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_Naive_1-DC_d3.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_Naive_1-LEC_d1.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_Naive_1-LEC_d2.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_genes_differential_Naive_1-LEC_d3.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_DC_d1-DC_d2.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_DC_d1-DC_d3.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_DC_d2-DC_d3.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_LEC_d1-DC_d1.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_LEC_d1-DC_d2.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_LEC_d1-DC_d3.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_LEC_d1-LEC_d2.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_LEC_d1-LEC_d3.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_LEC_d2-DC_d1.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_LEC_d2-DC_d2.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_LEC_d2-DC_d3.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_LEC_d2-LEC_d3.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_LEC_d3-DC_d1.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_LEC_d3-DC_d2.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_LEC_d3-DC_d3.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_Naive_1-DC_d1.txt.gz |
2.8 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_Naive_1-DC_d2.txt.gz |
2.8 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_Naive_1-DC_d3.txt.gz |
2.8 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_Naive_1-LEC_d1.txt.gz |
2.8 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_Naive_1-LEC_d2.txt.gz |
2.8 Mb |
(ftp)(http) |
TXT |
| GSE88830_transcripts_differential_Naive_1-LEC_d3.txt.gz |
2.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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