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Series GSE152888 Query DataSets for GSE152888
Status Public on Oct 28, 2020
Title Targeted single cell RNA sequencing of T cells infiltrated in mouse gastric cancer.
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary YTN2 and YTN16 cells are chemically induced gastric cancer cell lines. YTN2 is spontaneously regressed in C57BL/6 mice in CD8+ T cell-dependent manner, while YTN16 grows progressively. To investigate tumor infiltrating T cells, we performed single-cell RNA-Seq of CD4+ and CD8+ T cells in YTN2 and YTN16 gastric tumor-bearing mice for 44 T cell-related genes (Supplementary Table 1).
 
Overall design Mice were inoculated with 5 ×106 YTN2 or YTN16 on day 0. Tumors were harvested on day 7 and CD4+ and CD8+ T cells were sorted. Single-cell RNA-Seq was performed using vertical flow array chips (Shirai et al, Scientific Reports, 6, srep36014, 2016).
 
Contributor(s) Nagaoka K, Shirai M, Kakimi K
Citation(s) 33093158
Submission date Jun 20, 2020
Last update date Oct 28, 2020
Contact name Koji Nagaoka
Organization name The Tokyo University Hospital
Department Department of Immunotherapeutics
Street address 7-3-1 Hongo, Bunkyo-ku
City Tokyo
ZIP/Postal code 113-8655
Country Japan
 
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (1)
GSM4629065 Single-cell RNA-Seq of Tumor-infiltrating T cells
Relations
BioProject PRJNA640802
SRA SRP268139

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE152888_RAW.tar 100.0 Kb (http)(custom) TAR (of TXT)
GSE152888_Supplementary_Table_1._Genes_analyzed_in_the_single-cell_RNA-Seq.xlsx 15.3 Kb (ftp)(http) XLSX
GSE152888_Supplementary_Table_2._RT_probes_immobilized_to_microchambers_of_VAFC.xlsx 16.5 Kb (ftp)(http) XLSX
GSE152888_Supplementary_Table_3._Primers_for_1st_PCR.xlsx 14.6 Kb (ftp)(http) XLSX
GSE152888_Supplementary_Table_4._Primers_for_2nd_PCR.xlsx 14.7 Kb (ftp)(http) XLSX
GSE152888_Supplementary_Table_5._Primers_for_3rd_PCR.xlsx 12.8 Kb (ftp)(http) XLSX
GSE152888_Supplementary_Table_6._Information_of_cells_on_each_chip.xlsx 9.6 Kb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data provided as supplementary file

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