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| Status |
Public on Sep 06, 2023 |
| Title |
wu16,scRNA-seq |
| Sample type |
SRA |
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| Source name |
Pancreas
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Pancreas
ajcc stage: Stage IIA (cT3N0M0)
tumor location: Body/Tail
pathology: Adenocarcinoma
vital status_(1_dead,_0_alive): 1
survival time_(days): 213
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| Extracted molecule |
total RNA |
| Extraction protocol |
For EUS-FNB samples, endoscopic ultrasound was performed on patients with suspected solid pancreatic masses based on CT or MRI imaging. The diagnosis of pancreatic adenocarcinoma was confirmed by formal pathologic evaluation. After clinical diagnostic tissue acquisition was completed with 2-3 passes of a 22-gauge needle, an additional pass was obtained with a backfin “fine-needle biopsy” (FNB) needle.
Tissue was carefully washed with cold PBS, collected in RPMI 1640 media (Gibco) on ice when processed fresh, or collected in freezing media (90%FBS + 10% DMSO, when processed at a later time point) and dissociated into single cell suspension both mechanically and enzymatically as previously described40. Resected surgical tumor tissue was also dissociated in a similar way to obtain single-cell suspensions. Subsequently, single-cell suspensions were diluted to a final concentration of ~1,000 cells/μl and sequencing libraries prepared using the 10x Genomics Chromium Single Cell 5’ library platform. Complementary DNA libraries were then sequenced on an Illumina NovaSeq S4 flow cell with a target of 50,000 reads/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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| Description |
10x Genomics
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| Data processing |
We aligned reads to the GRCh38 reference genome and obtained gene expression counts using 10x Cell Ranger 3.0.2 with default parameters. FASTQ files were aligned to the GRCh38 reference genome with the STAR aligner. Cell-specific unique molecular identifiers (UMIs) were then used to generate gene expression matrices.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files (RNA count matrices).
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| Submission date |
Sep 02, 2023 |
| Last update date |
Sep 29, 2023 |
| Contact name |
Erik Storrs |
| E-mail(s) |
estorrs@wustl.edu
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| Organization name |
Washington University
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| Street address |
660 S Euclid Ave
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| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE242230 |
High-dimensional deconstruction of pancreatic cancer identifies tumor microenvironmental and developmental stemness features that predict survival |
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| Relations |
| BioSample |
SAMN37253800 |
| SRA |
SRX21607696 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7755920_wu16_barcodes.tsv.gz |
2.2 Mb |
(ftp)(http) |
TSV |
| GSM7755920_wu16_features.tsv.gz |
264.3 Kb |
(ftp)(http) |
TSV |
| GSM7755920_wu16_matrix.mtx.gz |
12.5 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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