|
| Status |
Public on Feb 16, 2022 |
| Title |
BPH, 10X Chromium platform, v3.1 [047563_1562-all-cells_cDNA] |
| Sample type |
SRA |
| |
|
| Source name |
whole cell
|
| Organism |
Homo sapiens |
| Characteristics |
tissue id: 047563_1562-all-cells
sample type: mRNA from whole cell
cell type: all BPH associated cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Human BPH tissue was minced and then digested in 1000 U/mL Collagenase I + 1 mg/mL DNAse in HBSS while shaking at 37 degrees C for 4 hours. Digested samples were further incubated with TrypLE Express for 5 min while shaking at 37 degrees C. Samples were washed, red blood cells lysed, and debris removal completed with Miltenyi kit prior to loading onto the 10X Chromium.
Libraries were prepared following the protocol for mRNA sequencing (10x Chromium), v3.0 or v3.1.
RNA sequencing on an Illumina NovaSeq 6000 next generation sequencer
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
047563_1562-all-cells
047563_1562_cDNA_S2
|
| Data processing |
FastQC v.0.11.3 was used to observe read quality
Cellranger v.3.0.0 was used to do initial quality control, alignment, and counting
Seurat was used to normalize, cluster, identify marker genes and perform DE analysis.
Genome_build: Ensembl Genome Reference Consortium Human Build 38 (GRCh38.p3)
Supplementary_files_format_and_content: raw measurements for 10x Genomics data (filtered to contain only detected cellular barcodes)
|
| |
|
| Submission date |
Sep 08, 2021 |
| Last update date |
Feb 16, 2022 |
| Contact name |
Nadia Marie Atallah |
| Organization name |
Purdue University
|
| Department |
Center for Cancer Research
|
| Street address |
201 S. University St
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN21357410 |
| SRA |
SRX12102952 |
