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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 22, 2022 |
| Title |
TRAMPTIM3.2 |
| Sample type |
SRA |
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| Source name |
Tumor
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| Organism |
Mus musculus |
| Characteristics |
tissue: Tumor
cell type: Endo CD8 T cell
sequencing batch: 4
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cell sorting was performed by FACS Aria II (BD Biosciences). For RNA-seq of P14s in LCMV Arm or in TRAMPC1-GP bearing mice, Live, CD4-CD14-CD19-, CD45.1+CD8+CD44+PD1+ were sorted. For RNA-seq of endogenous CD8 T cells from tumor, Live, CD4-CD14-CD19-Ly6G-, CD8+CD44+PD1+ 127+ or TIM3+ were sorted. performed by FACS Aria II (BD Biosciences). For RNA-seq of P14s in LCMV Arm or in TRAMPC1-GP bearing mice, Live, CD4-CD14-CD19-, CD45.1+CD8+CD44+PD1+ were sorted. For RNA-seq of endogenous CD8 T cells from tumor, Live, CD4-CD14-CD19-Ly6G-, CD8+CD44+PD1+ 127+ or TIM3+ were sorted. Qiagen micro RNA/DNA all prep columns were used for RNA extraction.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
P14 TCR transgenic CD8 T cells specific for GP33 epitope of LCMV. Activated P14s sorted from LCMV Armstrong infection, TDLN and tumor of TRAMPC1-GP bearing mice, or naïve spleen.
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| Data processing |
Aligned with HISAT2
Reads counted with subread/featurecounts
normalization and differential expression with DESEQ2
Assembly: mm10
Supplementary files format and content:CSV file with raw counts for all genes and samples
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| Submission date |
Dec 20, 2022 |
| Last update date |
Jan 04, 2023 |
| Contact name |
Haydn Kissick |
| E-mail(s) |
haydn.kissick@emory.edu
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| Phone |
6172598364
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| Organization name |
Emory University
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| Street address |
1462 Clifton Rd
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| City |
Atlanta |
| State/province |
Georgia |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE216731 |
LN-stem, tumor stem, tumor terminally differentiated CD8 T cells from human kidney cancer |
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| Relations |
| BioSample |
SAMN32330219 |
| SRA |
SRX18916803 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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