|
| Status |
Public on Mar 15, 2022 |
| Title |
Short Frozen 2a |
| Sample type |
SRA |
| |
|
| Source name |
testis
|
| Organism |
Rattus rattus |
| Characteristics |
replicate: 2
treatment: Short Frozen
selection: EpCAM+
|
| Treatment protocol |
Cells for transplantation or encapsulation were either used fresh, frozen for 1-4 months or frozen for 23+ years. Cells were used unselected or following EpCAM MACS antibody selection.
|
| Growth protocol |
Fresh tissue from rat testes were used as appropriate. Cells were digested in collagenase, trypsin and Miltenyi Dead Cell Removal Kit before encapsulation. For transplantation experiments, EpCAM+ cells were used to transplant into J:Nu nude mice and allowed to grow for 2+ months before being harvested in the same manner.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were encapulated in a salinized chip and RT reaction was performed at 70°C instead of 65°C but otherwise followed the inDrops protocol.
Library generated per inDrops protocol. Sequenced on NextSeq500 (Illumina) 75 cycle-cycle high output to depth of approximately 30k reads per cell
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Fastq files generated with BaseSpace (Illumina)
Count matricies generated with indrops.py (github.com/indrops) using the rat and mouse genome builds listed below using Bowtie v1.2.3. These are the processed files listed above (i.e. tsv files)
QC, filtering and UMAP generated with Seurat v.3.1
Pseudotime generated with Monocle v3
Pathway analysis using Ingenuity Pathway Analysis (Qiagen)
Genome_build: Rattus norvegicus 6.0 DNA primary assembly (Rattus_norvegicus.Rnor_6.0.dna_sm.primary_assembly.fa.gz) along with the corresponding GTF file (Rattus_norvegicus.Rnor_6.0.85.gtf.gz) from Ensembl along with the Mus_musculus.GRCm38.dna_sm.primary_assembly.fa and Mus_musculus.GRCm38.85.gtf.gz GTF files for mouse.
Supplementary_files_format_and_content: csv file containing contrasts between each treatment and the 0ng FGF control
|
| |
|
| Submission date |
Aug 19, 2021 |
| Last update date |
Jul 10, 2024 |
| Contact name |
Eoin Christopher Whelan |
| E-mail(s) |
ewhelan@vet.upenn.edu
|
| Phone |
2158988805
|
| Organization name |
University of Pennsylvania School of Veterinary Medicine
|
| Department |
Biomedical Sciences
|
| Lab |
Sasaki
|
| Street address |
3800 Spruce St
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL28964 |
| Series (1) |
| GSE182438 |
Re-establishment of spermatogenesis after more than 20 years of cryopreservation of rat spermatogonial stem cells reveals an important impact in differentiation capacity |
|
| Relations |
| BioSample |
SAMN20862295 |
| SRA |
SRX11826210 |
