|
| Status |
Public on Jul 20, 2017 |
| Title |
P0testis_mRNA_seq: Pld6 KO, biological replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
P0testis
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/J
cell/tissue: whole testes
genotype: Pld6 KO, biological replicate 1, read1
age: postnatal day 0
|
| Treatment protocol |
For spermatocyte samples, the leptotene/zygotene-stage germ cells were purified by FACS.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated by acid phenol extraction using Isogene (Nippon Gene) from new born testes (at P0) and FACS-purified L/Z spermatocytes at 3-4 weeks afetr birth
The libraries for polyA(+) RNA sequencing were prepared using TruSeq stranded mRNA LT Sample Prep kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
PE100bp
|
| Data processing |
Sequences were obtained by using HiSeq1500 (Rapid mode, yielding 9-40 million reads per sample)
Sequencing reads were mapped onto whole transcriptome (using a gtf file from iGenome) and whoke genome by Tophat.
The resulting bam files were used to calculate gene expression levels by Cuffdiff.
For the spematocyte data, reads mapped to a region overlapping a repeat sequence (Repeatmasker table from UCSC genome browser) were removed for the calculation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-divided text files including (1) gene name, (2) genotype, (3) replicate ID, (4) raw flags, (5) internal scaled frags, (6) external scaled frags, (7) FPKM, (8) effective length, and (9) status.
|
| |
|
| Submission date |
Jul 14, 2015 |
| 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) |
| GSE70889 |
Gene and retrotransposon expression analysis for WT, Pld6 KO, and Dnmt3l KO 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 |
SAMN03857939 |
| SRA |
SRX1096742 |
