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| 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
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| Overall design |
Whole testis mRNA profiles of juvenile wild type rhesus monkeys were generated by deep sequencing, in triplicate or quadruplicate, using Illumina NextSeq500.
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| Contributor(s) |
Sethi R, Walker W |
| Citation(s) |
28938749 |
| |
| Submission date |
Apr 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Uma Chandran |
| E-mail(s) |
chandran@pitt.edu
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| Phone |
412-648-9326
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| Organization name |
University of Pittsburgh
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| Department |
BioMedical Informatics
|
| Street address |
5150 Center Ave
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15232 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL21120 |
Illumina NextSeq 500 (Macaca mulatta) |
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| Samples (10)
|
| GSM2577463 |
TP07 Vehicle Treatment Illumina RNASeq |
| GSM2577464 |
TP08 48 h Gonadotropin Treatment Illumina RNASeq |
| GSM2577465 |
TP09 Vehicle Treatment Illumina RNASeq |
| GSM2577466 |
TP10 48 h Gonadotropin Treatment Illumina RNASeq |
| GSM2577467 |
TP11 Vehicle Treatment Illumina RNASeq |
| GSM2577468 |
TP12 48 h Gonadotropin Treatment Illumina RNASeq |
| GSM2577469 |
TP15 96 h Gonadotropin Treatment Illumina RNASeq |
| GSM2577470 |
TP16 96 h Gonadotropin Treatment Illumina RNASeq |
| GSM2577471 |
TP17 96 h Gonadotropin Treatment Illumina RNASeq |
| GSM2577472 |
TP18 96 h Gonadotropin Treatment Illumina RNASeq |
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| Relations |
| BioProject |
PRJNA382886 |
| SRA |
SRP103923 |
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