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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 30, 2023 |
| Title |
scRNA-seq 1 |
| Sample type |
SRA |
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| Source name |
lung adenocarcinoma
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| Organism |
Homo sapiens |
| Characteristics |
tissue: lung adenocarcinoma
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cancerous epithelial cells (n=3,754), as determined as those cells harboring large chromosomal aberrations from InferCNV analysis, were subset and re-clustered using the following parameters: Ngenes = 2,000, Npcs = 20, Res = 0.9, Kparam = 10 (script NI04). We found the differences in gene expression between the three treatment time points (TN, RD, and PD) using the Seurat function Find-Markers using the MAST test21 and sample_name as the latent variable. Three separate tests were used to ascertain the differences between: 1) TN and RD, 2) TN and PD and 3) RD and PD (TableS5). Resulting differential gene lists were then filtered to limit patient specific effects. This is achieved by setting a threshold for non-zero expressing cells per patient (RD = 3 of RD patients and PD = 6 of PD patients) and removing differentially expressed genes explained by less than the thresholds set. The top 100 genes from each comparison were manually curated to evaluate for pathway activation. Decreased expression could indicate lack of detection due to the stochasticity of scRNaseq and thus for analysis of activated pathways we focused on upregulated genes. Gene signatures (TableS2) were compiled using differential expressed as well as known cell marker genes. Specifically, the alveolar signature is made of differentially expressed AT1/AT2 genes among the cancer cell time point comparisons as well has additional known AT1/AT2 genes 22. The remaining signatures were identified directly from top differentially expressed genes.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Jun 26, 2023 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Yang Zhao |
| E-mail(s) |
szhaoy@126.com
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| Organization name |
Second affiliated hospital of Xi'an Jiaotong University
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| Department |
Oncology
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| Street address |
No.157, fifth west road
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| City |
Xi'an |
| State/province |
Shaanxi |
| ZIP/Postal code |
710004 |
| Country |
China |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE235782 |
A handful of hybrid EMT cells are characterized as the origin from lung adenocarcinoma |
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| Relations |
| BioSample |
SAMN35989217 |
| SRA |
SRX20785553 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7509499_1barcodes.tsv.gz |
60.3 Kb |
(ftp)(http) |
TSV |
| GSM7509499_1features.tsv.gz |
529.7 Kb |
(ftp)(http) |
TSV |
| GSM7509499_1matrix.mtx.gz |
93.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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