|
| Status |
Public on Jan 19, 2019 |
| Title |
PTM_1_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Peritubular myoid (PTM) cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Peritubular myoid (PTM) cells
cell subtype: Primary isolated cells
strain: C57BL/6J
|
| Treatment protocol |
No treatment
|
| Growth protocol |
The isolated primary cells were cultured in DMEM/F12 containing 10% fetal bovine serum (FBS) at 37°C with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRNzol (Tiangen, Beijing, China).
RNA libraries were prepared for sequencing using standard BGI protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
SOAPnuke: v1.5.2, -l 15 -q 0.2 -n 0.05
HISAT2: v2.0.4, --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Bowtie2: v2.2.5, -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
RSEM: v1.2.12, default
DEGseq: Fold Change >= 2 and Adjusted Pvalue <= 0.001
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs
|
| |
|
| Submission date |
Jan 18, 2019 |
| Last update date |
Jan 20, 2019 |
| Contact name |
Su-Ren Chen |
| E-mail(s) |
chensuren@ioz.ac.cn
|
| Organization name |
Institute of Zoology, Chinese Academy of Sciences
|
| Department |
State Key Laboratory of Stem Cell and Reproductive Biology
|
| Street address |
1Beichen West Road, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (2) |
| GSE125303 |
RNA-Seq of testicular peritubular myoid cells, other testicular cells, and other tissue smooth muscle-like cells |
| GSE125304 |
RNA-seq and miRNA-seq of testicular peritubular myoid cells, other testicular cells, and other tissue smooth muscle-like cells |
|
| Relations |
| BioSample |
SAMN10769185 |
| SRA |
SRX5260763 |
