|
| Status |
Public on Oct 09, 2017 |
| Title |
TP18 96 h Gonadotropin Treatment Illumina RNASeq |
| Sample type |
SRA |
| |
|
| Source name |
testis
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: testis
age: 14 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 |
SAMN06756512 |
| SRA |
SRX2737240 |
