|
| Status |
Public on Jul 03, 2014 |
| Title |
Knockout |
| Sample type |
SRA |
| |
|
| Source name |
Spermatogonial progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Testis
cell type: Postnatal SPCs
genotype: Dnmt3l knockout
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Postnatal SPCs were isolated from 8dpp testes. RNA was extracted using Ambion Tri-Reagent and two microgram RNA was used to create the construction of sequencing libraries.
Two microgram RNA was purified by using poly-T oligo-attached magnetic beads and mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments were end-repaired, a single A base addition, and adapter ligation. The products were then purified and enriched with PCR to create the final cDNA library. Paired-end 100 nucleotide reads from each mRNA library were obtained using HiScanSQ (Illumina Inc., CIC bioGUNE, Bilbao, Spain).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
Sample 2
|
| Data processing |
Basecalls performed using CASAVA version 1.9
Sequenced reads were mapped to mm10 whole genome using TopHat v2.0.8 with parameters -p 4 -G genes.gtf -r 50.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks v2.1.1.
The statistics significance was filtered with a 2-fold changed selection criterion of RPKM from the corresponding genes.
Genome_build: mm10
Supplementary_files_format_and_content: GTF files include FPKM values for each Sample.
|
| |
|
| Submission date |
Jan 27, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Shau-Ping Lin |
| E-mail(s) |
shaupinglin@ntu.edu.tw
|
| Organization name |
National Taiwan University
|
| Department |
Institute of Biotechnology
|
| Street address |
4F, No. 81, Chang-Xing St.,
|
| City |
Taipei City |
| State/province |
select a state |
| ZIP/Postal code |
106 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL16173 |
| Series (1) |
| GSE54411 |
DNMT3L promotes quiescence in postnatal spermatogonial progenitor cells |
|
| Relations |
| SRA |
SRX450264 |
| BioSample |
SAMN02596607 |
