|
| Status |
Public on Aug 16, 2017 |
| Title |
P6 control mouse testis RNA-seq rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse testes
|
| Organism |
Mus musculus |
| Characteristics |
tissue: mouse testes
cell type: control mouse testes
passage: P6 (6 days post-partum)
|
| Growth protocol |
The mice used in this study were B6D2F1 (C57BL/6×DBA2), DBA2 and C57BL6 strains.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from control and Mettl3 cKO mouse testes using the TRIzol (Invitrogen) reagent by following the company's manual.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
P6 control mouse testis RNA-seq rep1
|
| Data processing |
Basecalls performed by Casava using default settings
For RNA-Seq data, the clean reads were mapped to at mm9 genome assembly by HISAT2. Default parameters of HISAT2 were used except with the options “--dta-cufflinks” and “--rna-strandness RF” opening.
Reads with unique genome location were retained for gene expression calculation using Cufflinks (version 2.0.2) with the option “--GTF”. And the genes with no less than 0.5 FPKM in at least one samples were used for the differential expressed genes analysis.
Fragments per Kilobase of exon per Megabase of library size (FPKM) was calculated using Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: FPKM files estimated by Cufflinks
|
| |
|
| Submission date |
Jun 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Qi Zhou |
| E-mail(s) |
zhouqi@ioz.ac.cn
|
| Organization name |
Institute of Zoology,CAS
|
| Lab |
Zhou
|
| Street address |
Datun Road, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE99771 |
Transcriptome analysis of gene expression and single-nucleotide-resolution m6A sites in normal and mettl3 cKO testis samples (RNA-Seq) |
| GSE99773 |
Transcriptome analysis of gene expression and single-nucleotide-resolution m6A sites in normal and mettl3 cKO testis samples |
|
| Relations |
| BioSample |
SAMN07203111 |
| SRA |
SRX2892784 |
