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Sample GSM2577467 Query DataSets for GSM2577467
Status Public on Oct 09, 2017
Title TP11 Vehicle Treatment Illumina RNASeq
Sample type SRA
 
Source name testis
Organism Macaca mulatta
Characteristics tissue: testis
age: 15 months
genotype: wild type
Treatment protocol Pulsatile gonadotropin (FSH+LH)/vehicle infusion was performed for 48 or 96 h
Extracted molecule total RNA
Extraction protocol The right testis from each animal was rapidly divided into 10 fragments and snap-frozen in liquid nitrogen and stored at -80C until RNA extraction. Total RNA was isolated from the testes using Trizol reagent. TruSeq Stranded Total RNA library preparation was performed using 1ug total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Sequence reads were trimmed using Cutadapt v 1.9.1 (adapter and qual 13)
Reads of each sample were aligned to reference using Tophat v 2.1.1 associated with Bowtie v 2.2.8
Mapped Reads of each sample were assembled into transcripts using Cufflinks v 2.2.1 with reference guided approach and masking rRNA, tRNA and small RNA (length < 200 bp)
Assembled transcripts of each sample were merged into a single Cuffmerge assembly using a reference guided approach. Reference annotation without rRNA, tRNA, small RNA (length < 200 bp) and LOC106997702 gene was used
Read counts on the cuffmerge assembled genes were obtained using HTSeq v 0.6.1p1
Genes of the samples were filtered (raw CPM > 1 for any 3 samples), library normalized (TMM), expression values as normalized CPM calculated and differential expression analyzed (exactTest) using edgeR
Genome_build: rheMac8
 
Submission date Apr 14, 2017
Last update date May 15, 2019
Contact name Uma Chandran
E-mail(s) chandran@pitt.edu
Phone 412-648-9326
Organization name University of Pittsburgh
Department BioMedical Informatics
Street address 5150 Center Ave
City Pittsburgh
State/province PA
ZIP/Postal code 15232
Country USA
 
Platform ID GPL21120
Series (1)
GSE97786 The juvenile rhesus monkey (Macaca mulatta) testicular transcriptome and differential gene expression associated with the decision of undifferentiated spermatogonia to commit to the differentiation pathway
Relations
BioSample SAMN06756517
SRA SRX2737235

Supplementary file Size Download File type/resource
GSM2577467_TP11_NextSeq_rheMac8-ncbi_tophat_sorted.bedgraph.gz 514.0 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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