|
| Status |
Public on Dec 16, 2021 |
| Title |
BPH559PrF |
| Sample type |
SRA |
| |
|
| Source name |
OCT Frozen BPH Tissue
|
| Organism |
Homo sapiens |
| Characteristics |
patient phenotype: BPH
prostatic zone: Transition Zone
tissue: prostate
|
| Treatment protocol |
Tissues obtained fresh from simple prostatectomies on BPH patients were embedded in OCT.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Slides were processed using 10x Genomics Visium Fresh-Frozen Spatial Gene Expression protocol (3' v1 with H&E).
According to 10x Genomics’ protocol, sequenced PE150 on a NovaSeq 6000
spatialRNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ spaceranger mkfastq version 1.2.0 was used to demultiplex fastqs using default settings
10x Genomics’ spaceranger count version 1.2.0 was used to generate mapped bam files using default settings combining fastq's from NovaSeq 6000
Genome_build: GRCh38
Supplementary_files_format_and_content: Genes-by-cells matrix in Hierarchical Data Format 5 File (H5) and H&E image files (png)
|
| |
|
| Submission date |
Jun 25, 2021 |
| Last update date |
Dec 16, 2021 |
| Contact name |
Gervaise H. Henry |
| E-mail(s) |
[email protected]
|
| Phone |
2146480497
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Urology
|
| Lab |
Strand Lab
|
| Street address |
5323 Harry Hines Blvd, Mail Code:9110
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE178934 |
Human prostate luminal epithelia adopt a club-like state in response to low androgen levels |
| GSE179615 |
Human prostate luminal epithelia adopt a club-like state in response to low androgen levels (spatial and single-cell transcriptomics) |
|
| Relations |
| BioSample |
SAMN19876796 |
| SRA |
SRX11230367 |
