|
| Status |
Public on Jan 13, 2020 |
| Title |
7yo_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Testicular cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Testicle
age: 7
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Testicular tissues were firstly minced into small pieces mechanically, and subject to trypsin digestion for ~25 min at 37 C. Cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/ul, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 13 cycles used for cDNA amplification and 12 cycles for library amplification, which was then sequenced on a 26 X 100 cycle paired-end run via a Illumina 2500 instrument. Each sample was sequenced in one separate sequencing lane.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file:
Pubertal_combined_UMI.txt.gz
column header naming format:
Y7-barcode_sequence-2
|
| Data processing |
Samples were sequenced as paired end sequencing. Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v2.2.0). Fastq files were then run with count application (Cell Ranger v2.2.0) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and single cells that passed filtering
|
| |
|
| Submission date |
Jul 11, 2019 |
| Last update date |
Jan 13, 2020 |
| Contact name |
Jingtao Guo |
| E-mail(s) |
jingtao.guo@hci.utah.edu
|
| Phone |
801-585-1823
|
| Organization name |
University of Utah School of Medicine
|
| Department |
Department of Surgery Division of Urology
|
| Lab |
Jingtao Guo
|
| Street address |
2000 Circle of Hope
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE134144 |
The Dynamic Transcriptional Cell Atlas of Testis Development During Human Puberty |
|
| Relations |
| BioSample |
SAMN12255159 |
| SRA |
SRX6431153 |
