|
| Status |
Public on Jul 20, 2017 |
| Title |
small_RNA_seq: spermatogonia, biological replicate 1, technical replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
male germ cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/J
isolation: FACS with Hoechst-33342 staining
Stage: spermatogonia
age: postnatal 3-4wks
|
| Treatment protocol |
Total RNA was isolated by acid phenol extraction using Isogene (Nippon Gene) from FACS-purified spermatogonia and spermatocytes (L/Z)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
standard procedure involving phenol/chloroform extraction, and isopropanol precipitation
The libraries were prepared using TruSeq Small RNA Sample Prep kit (Illumina)
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
SE100bp
|
| Data processing |
The same libraries were sequenced twice (technical replicates 1 and 2)
The sequencing methods for technical replicate 1 ; sequenced by HiSeq2500 (Rapid mode for 50-bp single-end sequencing, yielding 4-8 million reads per sample)
The sequencing methods for technical replicate 2 ; sequenced by HiSeq1500 (High-output mode for 100-bp single-end sequencing, yielding 4-8 million reads per sample)
The adaptor sequence was trimed by cutadapt, and read numbers for each insert sequence were counted
The sequences were mapped to the consensus sequences of mouse retrotransposons using Seqmap allowing 2-bp missmatches.
Genome_build: repeatmaskerlibraries-20130422
Supplementary_files_format_and_content: tab-divided text files for sequence read numbers and comma-divided text files for rpm values for each retrotransposon.
|
| |
|
| Submission date |
Mar 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kota Inoue |
| E-mail(s) |
inoue@bioreg.kyushu-u.ac.jp
|
| Phone |
+8192-642-6760
|
| Organization name |
Kyushu University
|
| Department |
Medical Institute of Bioregulation
|
| Lab |
Division of Epigenomics and Development
|
| Street address |
3-1-1 Maidashi, Higashiku
|
| City |
Fukuoka |
| ZIP/Postal code |
812-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE70890 |
Small RNA sequencing analysis for male germ cells during spermatogenesis |
| GSE70891 |
The effect of the Pld6 and Dnmt3l mutations on DNA methylation and expression of retrotransposons in mouse male germ cells |
|
| Relations |
| BioSample |
SAMN04532049 |
| SRA |
SRX1613274 |
