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| Status |
Public on Oct 10, 2023 |
| Title |
patient2_NN |
| Sample type |
SRA |
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| Source name |
Prostate
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Prostate
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| Extracted molecule |
total RNA |
| Extraction protocol |
Human prostate tissues were first digested in aDMEM/F12/Collagenase II (1.5mg/ml)/Hyaluronidase VIII (1000 u/ml; Thermo Fisher Scientific) plus 10 μM Y-27632 (Tocris) for 1 hour at 37°C with 1500 rpm mixing, continuously agitated. Subsequently, after centrifuging at 150 g for 5 min at 4°C, digested cells were suspended in 1 ml TrypLE with 10 µM Y-27632 and digested for 15 min at 37°C and neutralized in aDMEM/F12/FBS (0.05%). Dissociated cells were subsequently passed through 70 μm and 40 μm cell strainers (BD Biosciences, San Jose, CA) to get single cells. Samples were resuspended in 1x PBS and sorted for DAPI to enrich living cells.
Barcoded cDNA libraries were created from single-cell suspensions using the Chromium Single Cell 3’ Library and Gel Bead Kit, and Chip Kit from 10x Genomics70, according to manufacturer recommendations. 8,000-16,000 cells were targeted for 3’ RNA library preparation, multiplexed in an Illumina NovaSeq 6000, and sequenced at an average depth of 25,000 reads per cell.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Expression matrices were generated from raw Illumina sequencing output using CellRanger. Bcl files were demultiplexed by bcl2fastq, then reads were aligned to GRCh38 using STAR. The expression matrices from the nine human samples were concatenated into a single count matrix.
Assembly: hg38
Supplementary files format and content: anndata (annotated data matrix) object saved in h5ad-file format. The file contains the preprocessed, normalized and annotated count data of the stromal cells derived from the human data.
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| Submission date |
Sep 28, 2023 |
| Last update date |
Oct 10, 2023 |
| Contact name |
Mohamed Omar |
| E-mail(s) |
mao4005@med.cornell.edu
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| Organization name |
Weill Cornell Medicine
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| Department |
Department of Pathology and Laboratory Medicine
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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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| Platform ID |
GPL24676 |
| Series (2) |
| GSE244267 |
Distinct mesenchymal cell states mediate prostate cancer progression (human) |
| GSE244270 |
Distinct mesenchymal cell states mediate prostate cancer progression |
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| Relations |
| BioSample |
SAMN37595780 |
| SRA |
SRX21924099 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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