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Series GSE97786 Query DataSets for GSE97786
Status Public on Oct 09, 2017
Title 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
Organism Macaca mulatta
Experiment type Expression profiling by high throughput sequencing
Summary Goal: To identify the genes associated with the decision of undifferentiated spermatogonia to commit to a pathway of differentiation.
Methods: testis mRNA profiles of 10 juvenile wild-type rhesus monkeys (3 vehicle-treated; 6 gonadotropin treated) were generated by deep sequencing, in triplicate and quadruplicate, using Illumina NextSeq500. The sequence reads that passed filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: We mapped about 45-55 million sequence reads per sample to the rhesus monkey genome (rheMac 8.0.1) and identified 26,813 transcripts in the testes of wild type monkeys with TopHat workflow. Approximately a combined 7% of unique transcripts showed differential expression between vehicle and gonadotropin treatment for 48 and 96h, with a fold change ≥1.5 and p value <0.05. Altered expression of 12 genes was confirmed with qRT–PCR, substantiating the RNA-seq findings.
Conclusions: The testis transcriptome of the juvenile monkey contained 15,475 genes of which 15,174 were protein encoding genes or pseudogenes. Gonadotropin stimulation for 48 h resulted in the commitment of spermatogonia to differentiate and this was associated with the emergence of 1587 differentially expressed genes.
Funding support: NIH R01 HD072189 to Tony Plant
Overall design Whole testis mRNA profiles of juvenile wild type rhesus monkeys were generated by deep sequencing, in triplicate or quadruplicate, using Illumina NextSeq500.
Contributor(s) Sethi R, Walker W
Citation(s) 28938749
Submission date Apr 14, 2017
Last update date May 15, 2019
Contact name Uma Chandran
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
Platforms (1)
GPL21120 Illumina NextSeq 500 (Macaca mulatta)
Samples (10)
GSM2577463 TP07 Vehicle Treatment Illumina RNASeq
GSM2577464 TP08 48 h Gonadotropin Treatment Illumina RNASeq
GSM2577465 TP09 Vehicle Treatment Illumina RNASeq
BioProject PRJNA382886
SRA SRP103923

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE97786_RAW.tar 4.3 Gb (http)(custom) TAR (of BEDGRAPH)
GSE97786_Ramaswamy_et_al-SUPPLEMENTARY_TABLE-III-Transcriptome.txt.gz 819.0 Kb (ftp)(http) TXT
GSE97786_TP_NextSeq-rheMac8-ncbi_edgeR-exactTest.txt.gz 7.7 Mb (ftp)(http) TXT
GSE97786_TP_NextSeq_rheMac8-ncbi_Cuffmerge.gtf.gz 15.0 Mb (ftp)(http) GTF
GSE97786_TP_NextSeq_rheMac8-ncbi_Cuffmerge_no-strand.fa.gz 54.4 Kb (ftp)(http) FA
GSE97786_TP_NextSeq_rheMac8-ncbi_Cuffmerge_strand.fa.gz 99.8 Mb (ftp)(http) FA
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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