|
| Status |
Public on Jul 07, 2021 |
| Title |
musAd002_UrF_re-analyzed |
| Sample type |
SRA |
| |
|
| Source name |
Mouse urethra
|
| Organism |
Mus musculus |
| Characteristics |
digestion enzyme: 10mg/mL Cold Protease 1hr
number of mice pooled: 1
macs strategy: NONE
10x library type: 3'GEXv2
|
| Treatment protocol |
Single-cells were dissociated from health adult mouse urethra
|
| 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 and v3 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 |
re-analysis of GSM4338168
|
| Data processing |
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ cellranger mkfastq version 4.0.0 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 4.0.0 was used to generate mapped bam files using default settings combining fastq's from NextSeq 500 and NovaSeq 6000
Genome_build: mm10
Supplementary_files_format_and_content: Genes-by-cells matrix in Hierarchical Data Format 5 File (H5)
|
| |
|
| Submission date |
Apr 21, 2021 |
| Last update date |
Jul 07, 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 |
GPL19057 |
| Series (2) |
| GSE172515 |
Single-cell RNA-sequencing of adult mouse urethra v2 |
| GSE173096 |
Single-cell RNA-sequencing of adult mouse lower urinary tracts v2 |
|
| Relations |
| Reanalysis of |
GSM4338168 |
| BioSample |
SAMN18823089 |
| SRA |
SRX10653851 |
