|
| Status |
Public on Jul 20, 2017 |
| Title |
Dnmt3L_KO_mRNA_seq |
| Sample type |
SRA |
| |
|
| Source name |
Spermatocyte
|
| Organism |
Mus musculus |
| Characteristics |
strain: F1 hybrid between C57BL6/J and MSM/Ms
cell/tissue: FACS-purified L/Z spermatocytes
genotype: Dnmt3L_KO
age: postnatal 3-4wks
|
| 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 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 |
SE50bp
|
| Data processing |
Sequences were obtained by using HiSeq1500 (Rapid mode, yielding 55-92 million reads per sample)
Sequencing reads were mapped onto whole transcriptome (using a gtf file from iGenome) and whole genome by Tophat.
The resulting bam files were used to calculate gene expression levels by Cuffdiff.
SNPSplit was used to discriminate the derived alleles.
Cuffdiff was used to calculate the allele frequencies.
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 |
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) |
| GSE70891 |
The effect of the Pld6 and Dnmt3l mutations on DNA methylation and expression of retrotransposons in mouse male germ cells |
| GSE78905 |
Gene and retrotransposon expression analysis in the F1 hybrid background of B6 and MSM for WT, Pld6 KO, and Dnmt3l KO male germ cells |
|
| Relations |
| BioSample |
SAMN04532052 |
| SRA |
SRX1613288 |
