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| Status |
Public on Jan 14, 2020 |
| Title |
The single cell transcriptional landscape of human lung adenocarcinoma (primary tumours and metastases) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
By transcriptionally profiling single cells from patients spanning different stages of lung adenocarcinoma progression, we provide evidence of epithelial regeneration in untreated primary tumours and a continuum of phenotypic states spanning key stages of embryonic development and lung morphogenesis in metastases. We transcriptionally profiled 41,384 single cells obtained from fresh surgical human samples taken from non-tumour-involved lung (n = 4), primary lung adenocarcinomas (n = 8; 7 untreated and 1 post neo-adjuvant chemotherapy), as well as brain (n = 3), bone (n = 1), and adrenal (n = 1) lung adenocarcinoma metastases. These samples were derived from patients spanning various stages of tumour progression without enrichment for a specific cell type, such that the entire tumour and its microenvironment were sampled in an unbiased manner. Data from all patients were merged to create a global cell atlas of the normal lung, primary tumours, and metastases.
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| Overall design |
Single-cell RNA sequencing was performed on 17 donors using the 10X Genomics protocol. For each donor, all viable cells (identified by forward and side scatter and DAPI exclusion) were assayed for trancriptome-wide RNA-sequence.
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| Contributor(s) |
Laughney AM, Hu J, Campbell NR, Bakhoum SF, Setty M, Lavallée VP, Xie Y, Masilonis I, Carr AJ, Allaj V, Mattar M, Xavier J, Mazutis L, Poirier JT, Rudin CM, Pe'er D, Massagué J |
| Citation(s) |
32042191 |
| Submission date |
Dec 16, 2018 |
| Last update date |
Apr 01, 2020 |
| Contact name |
Ashley M Laughney |
| E-mail(s) |
ashley.laughney@gmail.com
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| Organization name |
Weill Cornell Medicine
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| Department |
Physiology, Biophysics and Systems Biology
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| Lab |
Laughney Lab
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| Street address |
413 East 69th Street
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| City |
NEW YORK |
| State/province |
New York |
| ZIP/Postal code |
10021 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (17)
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| This SubSeries is part of SuperSeries: |
| GSE123904 |
The single cell transcriptional landscape of lung adenocarcinoma metastasis |
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| Relations |
| BioProject |
PRJNA510251 |
| SRA |
SRP173552 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE123902_GEO_README.rtf |
1.4 Kb |
(ftp)(http) |
RTF |
| GSE123902_RAW.tar |
90.4 Mb |
(http)(custom) |
TAR (of CSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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