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Sample GSM4079807 Query DataSets for GSM4079807
Status Public on Dec 31, 2020
Title Immature testes-2 mRNAseq
Sample type SRA
 
Source name immature bovine testes
Organism Bos taurus
Characteristics breed: Chinese Red Steppes cattle
tissue: immature testes
Growth protocol A total of 6 testicular tissues of cattle (3 newborn for 1-day and 3 adult for 24-months-old) were collected from the Agricultural Science Academy of Jilin Province cattle farm (Gongzhuling, China).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the collected testis tissues using trizol reagent (Invitrogen, USA) following the manufacturer’s instructions. Total RNA was treated with DNase I (NEB, Beijing, China). The RNA concentration and integrity quality were detected using an Agilent 2100 Bioanalyzer (Agilent technologies, Palo Alto, CA) and the RIN or RNA integrity number was used to determine the RNA integrity quality of extraction.
Six libraries of RNA-seq were constructed and grouped to I and M by source of testicular tissues for subsequent analysis. mRNA was enriched with oligo (dT) beads and fractionized for cDNA synthesis. The cDNA was then amplified to prepare the mRNA library. Two small RNA libraries representing each group (coming from the pooling of testis tissues in 3 newborn for 1-day and 3 adult for 24-months-old cattle) were constructed for Solexa sequencing according to the Illumina® TruSeq™ Small RNA Sample manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Male reproduction
Data processing Whole transcriptome libraries preparation and deep sequencing
The sequencing library of each RNA sample was pre- pared by using Ion Total RNA-Seq Kit v2
Raw Data Treatment: Using high-throughput Life technologies Ion Proton Sequencer, the transcript with poly (A)+ RNA of Human were analyzed. Reads sequenced were filtered and mapped to Cattle genome (download from NCBI) using Mapsplice software. The mapped reads was counted to achieve the expression of each gene based on the gene annotation information from NCBI database.
Data Filtering:In order to achieve the best quality of the RNA Sequencing, Novelbio applied the reads filtration to filter the reads with lower quality and short sequence under following criteria: read length > 50; over 30% base quality >13.
Identification of differentially expressed genes :The DE-Seq algorithm was applied to filter differentially expressed genes. After the significance analysis and FDR (false discovery rate) analysis , we selected the differentially expressed genes according to the FDR threshold set at p < 0.05 and FDR <0.05. And the fold changes of any two groups are more than 2.
All target genes regulated by DERs were predicted by the combination of miRbase (http://www.mirbase.org) and TargetScan (http://www.targetscan.org). All the predicted target genes were intersected with the DEGs obtained by RNA-seq, and then the DEGs and DERs were obtained by a combined analysis.
Genome_build: Btau_5.0.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ..
 
Submission date Sep 16, 2019
Last update date Dec 31, 2020
Contact name Xibi Fang
E-mail(s) fangxibi@yeah.net
Organization name Jilin University
Street address No. 5333 Xian Road
City Changchun
ZIP/Postal code 130062
Country China
 
Platform ID GPL15749
Series (1)
GSE137464 A comparative profile of the mRNA and microRNA transcriptome in immature and mature bovine testes
Relations
BioSample SAMN12758271
SRA SRX6852890

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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