|
| Status |
Public on Apr 28, 2020 |
| Title |
D35PrPzF_Via 2 |
| Sample type |
SRA |
| |
|
| Source name |
Viable human prostate peripheral zone
|
| Organism |
Homo sapiens |
| Characteristics |
patient phenotype: Donor (Normal)
prostatic zone: Peripheral Zone
digestion enzyme: 5mg/mL Collagenase I 4hr
facs ab profile: Via-
|
| Treatment protocol |
Populations of single-cells dissociated from health prostates from organ donors were isolated by FACS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell suspensions containing ~17400 cells were loaded on 10x Genomics Chromium single-cell Controller with 3’ library and gel bead kit v2 according to manufacture’s recommendations
According to 10x Genomics’ protocol, sequenced (R1=26cycles R2=58cycles, i7=8cycles on NextSeq 500) OR (PE150 on NovaSeq 6000)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Samples were sequenced on the Illumina NextSeq 500 and the Illumina NovaSeq 6000
Viable cells from normal human prostate tissue peripheral zone
|
| Data processing |
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ cellranger mkfastq version 3.1.0 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 3.1.0 was used to generate mapped bam files using default settings combining fastq's from NextSeq 500 and NovaSeq 6000
Genome_build: GRCh38
Supplementary_files_format_and_content: Genes-by-cells matrix in Hierarchical Data Format 5 File (H5)
|
| |
|
| Submission date |
Feb 24, 2020 |
| Last update date |
Apr 19, 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 |
GPL18573 |
| Series (2) |
| GSE145843 |
Single-cell RNA-sequencing of adult human prostates from organ donors |
| GSE145928 |
Single-cell RNA-sequencing of adult human prostates and urethra (normal and diseased) |
|
| Relations |
| Alternative to |
GSM3293887 |
| Reanalyzed by |
GSM5252461 |
| BioSample |
SAMN14175730 |
| SRA |
SRX7795678 |
