NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2652078 Query DataSets for GSM2652078
Status Public on Aug 16, 2017
Title P12 control mouse testis RNA-seq rep2
Sample type SRA
 
Source name mouse testes
Organism Mus musculus
Characteristics tissue: mouse testes
cell type: control mouse testes
passage: P12 (12 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 P12 control mouse testis RNA-seq rep2
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 SAMN07203108
SRA SRX2892789

Supplementary file Size Download File type/resource
GSM2652078_P12_Ctrl_2.fpkm_tracking.gz 654.0 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap