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Status |
Public on Jun 22, 2020 |
Title |
Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma [ST] |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
To define the cellular composition and spatial architecture of the tumor micoenvironment, we combined single-cell RNA-sequencing, spatial transcriptomics, and multiplexed ion-beam imaging from 10 patient cutaneous squamous cell carcinoma tumors and site-matched normal skin
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Overall design |
Patient tumors were fresh frozen and sectioned at 10um thickness onto spatial transcriptomics (ST) slides for mRNA capture, followed by library preparation and sequencing
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Contributor(s) |
Ji AL, Rubin AJ |
Citation(s) |
- Ji AL, Rubin AJ, Thrane K, Jiang S et al. Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. Cell 2020 Jul 23;182(2):497-514.e22. PMID: 32579974
- Chen L, Chang D, Tandukar B, Deivendran D et al. STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer. Genome Biol 2023 Nov 30;24(1):273. PMID: 38037084
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Submission date |
Jan 24, 2020 |
Last update date |
Dec 13, 2023 |
Contact name |
Andrew Ji |
E-mail(s) |
andrew.ji@mssm.edu
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Organization name |
Icahn School of Medicine at Mount Sinai
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Street address |
1428 Madison Ave.
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City |
New York |
State/province |
NY |
ZIP/Postal code |
10029 |
Country |
USA |
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Platforms (1) |
GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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Samples (16)
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This SubSeries is part of SuperSeries: |
GSE144240 |
Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma |
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Relations |
BioProject |
PRJNA603104 |
SRA |
SRP262989 |