|
| Status |
Public on Jan 15, 2017 |
| Title |
Cell 1 |
| Sample type |
SRA |
| |
|
| Source name |
Spermatogonia
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human spermatogonia
|
| Treatment protocol |
Cells picked from the sample were bathed in an additional rinse well containing cold PVS-BSA. Each cell was drawn into and expelled out of the microcapillary tube approximately three times before final capture. Finally, single cells were transferred to a sterile 0,2 ml thin-walled PCR tube in a 1,0 ul droplet of cold PBS-BSA. Cells were then either immediately processed for cDNA synthesis using previously published protocols (Tang et al., Nat Methods, 2011) or flash frozen in liquid nitrogen.
|
| Growth protocol |
For establishment of germ cell enriched cultures, testicular biopsies were enzymatically digested as previously published (Kossack et al. Hum Reprod. 2013). For enrichment of the germ cell population, cells in the supernatant were transferred to a separate cell culture dish, 18 hrs following plating of the initial cell suspension. Following 3-4 days of culture somatic and germ cells could be distinguished based on morphological characteristics, so that micromanipulation of selected spermatogonia could be performed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were made from 20 ng of double standed cDNA according to previous methods (Tang et al., Nat Methods, 2011).
Samples were barcoded and sequenced on an IonTorrent/Life Technologies Personal Genome Machine (PGM) 1.0 gig, 316 chip following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
| |
|
| Data processing |
TorrentSuite software (version 3.2, Ion Torrent/Life Technologies) was used for mapping the reads to the reference genome version hg19.
Resulting BAM files were used for plot coverage analysis.
Splus software was used to create coverage plots
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Splus software.The number of reads falling in the exons of the gene were counted and normalized by the size of the gene and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample
|
| |
|
| Submission date |
Dec 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Nina Neuhaus |
| E-mail(s) |
Nina.Neuhaus@ukmuenster.de
|
| Organization name |
University Hospital of Münster
|
| Department |
Centre of Reproductive Medicine and Andrology
|
| Street address |
Albert-Schweitzer-Campus 1, D11
|
| City |
Münster |
| ZIP/Postal code |
48151 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17301 |
| Series (1) |
| GSE91063 |
Single-cell Gene Expression Analysis Reveals Transcriptional Diversity among Human Spermatogonia |
|
| Relations |
| BioSample |
SAMN06126434 |
| SRA |
SRX2407259 |
