|
| Status |
Public on Apr 11, 2022 |
| Title |
1week_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
SSCs cultured for 1 week
|
| Organism |
Mus musculus |
| Characteristics |
culture time: 1 week
strain: DBA/2
cell type: spermatogonial stem cells (SSCs)
|
| Treatment protocol |
adult DBA/2 testicular cells purified by magnetically sorted using anti-CD9 antibody
|
| Growth protocol |
DBA/2 GS cells and adult DBA/2 testicular cells purified by magnetically sorted using anti-CD9 antibody were cultured in culture medium based on Iscove’s modified MEM (Invitrogen, Carlsbad, CA), which was supplemented with 10 ng/ml human FGF2, 15 ng/ml recombinant rat GDNF (both from Peprotech, London, UK) and 1% fetal bovine serum (FBS) (Kanatsu-Shinohara et al, 2014).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted by TRIzol (Qiagen) and purified by RNeasy mini kit (Qiagen)
RNA-seq libraries were generated from 200 ng total RNA with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls were performed using bcl2fastq v2.17.1.14.
The low-quality bases at the 3' read ends and the adaptor sequences were trimmed by cutadapt-1.16.
The ribosomal RNA (rRNA) sequence reads were filtered out using Bowtie 2.3.4.1.
The sequenced reads were mapped to the mm10 mouse reference genome using HISAT2 (version 2.1.0) with the mouse GENCODE (version M19) annotation gtf file.
The mapped reads with high mapping quality (MAPQ >= 20) were used for further analyses.
FPKM values were determined by Cuffdiff within Cufflinks version 2.2.1 package with the mouse GENCODE (version M19, protein_coding)
Genome_build: mm10
Supplementary_files_format_and_content: The tab-delimited text file include FPKM values for each sample.
|
| |
|
| Submission date |
Apr 11, 2019 |
| Last update date |
Apr 11, 2022 |
| Contact name |
Satoshi Watanabe |
| E-mail(s) |
watanabe.satoshi.7r@kyoto-u.ac.jp
|
| Phone |
81757514160
|
| Organization name |
Kyoto University
|
| Department |
Graduate School of Medicine
|
| Lab |
Department of Molecular Genetics
|
| Street address |
53, Kawahara-cho, Shogoin, Sakyo
|
| City |
Kyoto |
| State/province |
Kyoto |
| ZIP/Postal code |
606-8507 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE129658 |
Induced expression of PD-L1 in spermatogonial stem cells by self-renewal division allows allogeneic offspring production [Sequencing] |
| GSE129659 |
Induced expression of PD-L1 in spermatogonial stem cells by self-renewal division allows allogeneic offspring production |
|
| Relations |
| BioSample |
SAMN11398940 |
| SRA |
SRX5669424 |
