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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) |
32579974, 38037084 |
| 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 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE144239_RAW.tar |
222.1 Mb |
(http)(custom) |
TAR (of CSV, JPG, JSON, MTX, PNG, TSV) |
| GSE144239_ST_Visium_counts.txt.gz |
10.5 Mb |
(ftp)(http) |
TXT |
| GSE144239_ST_all_counts.txt.gz |
9.0 Mb |
(ftp)(http) |
TXT |
| GSE144239_ST_barcode_id.txt.gz |
16.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
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