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| Status |
Public on Aug 04, 2021 |
| Title |
Single cell RNA-sequencing of human brain metastasis-infiltrating T cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The goal of this study is to understand the biology of brain metastasis-infiltrating T cells.
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| Overall design |
Single cell suspensions were generated from surgically-resected metastatic brain tumors. For five patients (5, 14, 15, 16, and 17), tumor-infiltrating PD-1+ CD8 T cells were isolated by FACS from each patient, combined with patient-matched circulating naive CD8 T cells and subjected to scRNA-seq with VDJ sequencing. Hashing antibodies were used to distinguish naïve (Totalseq C0251) from tumor-infiltrating (Totalseq C0252) cells. Separate captures and sequencing libraries were generated for each patient. An additional scRNA-seq experiment was performed on pooled tumor-infiltrating total (CD4 + CD8) T cells from patient 16 (Totalseq C0251), patient 26 (Totalseq C0252), and patient 27 (Totalseq C0253). Circulating T cells were also sorted from a healthy donor and included with this experiment (Totalseq C0254). Cells were pooled, two captures were performed, and libraries were sequenced. In this latter experiment, cells were also stained with anti-CD8 Totalseq C0046, anti-CD4 Totalseq C0045, and anti-PD-1 biotin followed by streptavidin Totalseq C0961.
Please note that each processed data was generated from GEX, CITE-seq, and VDJ libraries, and is linked to the corresponding GEX sample records.
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| Contributor(s) |
Hudson WH |
| Citation(s) |
35584630, 35707680 |
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| Submission date |
Jul 03, 2021 |
| Last update date |
Jun 27, 2022 |
| Contact name |
William Hudson |
| Organization name |
Baylor College of Medicine
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| Department |
Molecular and Cellular Biology
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| Street address |
1 Baylor Plaza
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (21)
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| GSM5416355 |
Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 5) [GEX] |
| GSM5416356 |
Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 5) [CITE] |
| GSM5416357 |
Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 5) [VDJ] |
| GSM5416358 |
Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 14) [GEX] |
| GSM5416359 |
Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 14) [CITE] |
| GSM5416360 |
Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 14) [VDJ] |
| GSM5416361 |
Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 15) [GEX] |
| GSM5416362 |
Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 15) [CITE] |
| GSM5416363 |
Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 15) [VDJ] |
| GSM5416364 |
Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 16) [GEX] |
| GSM5416365 |
Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 16) [CITE] |
| GSM5416366 |
Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 16) [VDJ] |
| GSM5416367 |
Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 17) [GEX] |
| GSM5416368 |
Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 17) [CITE] |
| GSM5416369 |
Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 17) [VDJ] |
| GSM5416370 |
All tumor-infiltrating T cells from brain metastases (patients 16,26,27); pooled_capture 1 [GEX] |
| GSM5416371 |
All tumor-infiltrating T cells from brain metastases (patients 16,26,27); pooled_capture 1 [CITE] |
| GSM5416372 |
All tumor-infiltrating T cells from brain metastases (patients 16,26,27); pooled_capture 1 [VDJ] |
| GSM5416373 |
All tumor-infiltrating T cells from brain metastases (patients 16,26,27); pooled_capture 2 [GEX] |
| GSM5416374 |
All tumor-infiltrating T cells from brain metastases (patients 16,26,27); pooled_capture 2 [CITE] |
| GSM5416375 |
All tumor-infiltrating T cells from brain metastases (patients 16,26,27); pooled_capture 2 [VDJ] |
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| Relations |
| BioProject |
PRJNA743437 |
| SRA |
SRP326772 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE179373_RAW.tar |
216.6 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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