|
| Status |
Public on Sep 19, 2017 |
| Title |
Thy1_PRC1ctrl_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Thy1+ spermatogonia
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Thy1+ spermatogonia
strain: C57BL/6
tissue: testis
age: PND7
genotype: PRC1ctrl
biowardrobe ides: 2384
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using an RNeasy micro kit (Qiagen) according to the manual provided. RNA quality and quantity were checked using Bioanalyzer (Agilent) and Qubit (Life technologies), respectively. The initial amplification step was done with the NuGEN Ovation RNA-Seq System v2. The assay was used to amplify RNA samples to create double stranded cDNA. Libraries were then created by Nextera XT DNA Sample Preparation Kit (Illumina) and sequenced with Illumina HiSeq 2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Data analysis was performed using the BioWardrobe (PMID: 26248465 )
Briefly, reads were mapped to the mm10 genome and RefSeq-based transcriptome using RNA-STAR (v. 2.4.2a and assigned to the RefSeq genes using the BioWardrobe algorithm.
Genome_build: mm10
|
| |
|
| Submission date |
Aug 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
So Maezawa |
| E-mail(s) |
so.maezawa@cchmc.org
|
| Phone |
513-803-1377
|
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Reproductive Sciences
|
| Lab |
Namekawa lab
|
| Street address |
3333 Burnet Ave.
|
| City |
Cincinnati |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE102783 |
RNA-seq in spermatogonia from PRC1ctrl and dKO mice |
|
| Relations |
| BioSample |
SAMN07514891 |
| SRA |
SRX3101075 |
