|
| Status |
Public on Mar 30, 2016 |
| Title |
-TS3 |
| Sample type |
SRA |
| |
|
| Source name |
scapulohumeralis caudalis
|
| Organism |
Manacus vitellinus |
| Characteristics |
tissue: scapulohumeralis caudalis
treatment: in the absence of testosterone
|
| Treatment protocol |
1) golden-collared manakins: Each males were assigned at random to receive either a testosterone implant or a blank implant. Both testosterone-filled and control implants were inserted subcutaneously at the base of the neck according to standard procedures. 2) zebra finches: Each bird was assigned at random to receive either a flutamide implant or a blank implant. On the subsequent day, every male received an implant filled with testosterone.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from zebra finch and golden-collared manakin muscle tissues using Trizol (Life Technologies). Additional column purification and DNaseI treatment were applied using Direct-zol RNA kit (Zymo Research).
The standard Illumina protocol was used to prepare strand-specific libraries for RNA-Seq (TruSeq mRNA library prep kit, with ribosomal RNA removal and polyA selection).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava software used for basecalling.
Raw sequenced reads were trimmed for adaptor sequence using cutadapt, and then mapped to zebra finch whole genome, transcriptome (Ensembl annotations) and assembled golden-collared manakin genome using Bowtie version 0.12.9 with parameters --sam-nosq -S -k 80 –e 140 -n 3 -l 20 -q --phred33-quals -p 1 –y and BLAT version3.4 with parameters -minIdentity=75 -stepSize=75
Expression levels of genes, the RPKM (reads per kilobase of exon per million mapped reads) measure was calculated (MORTAZAVI et al. 2008)
Genome_build: taeGut1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
|
| |
|
| Submission date |
Oct 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jae-Hyung Lee |
| E-mail(s) |
jaehlee@khu.ac.kr
|
| Organization name |
Kyung Hee University
|
| Street address |
26 Kyungheedae-ro, Dongdaemun-gu
|
| City |
Seoul |
| ZIP/Postal code |
02447 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL20980 |
| Series (1) |
| GSE73660 |
Hormones, Genes, and Athleticism: Effect of Androgens on the Avian Muscular Transcriptome |
|
| Relations |
| BioSample |
SAMN04125366 |
| SRA |
SRX1299456 |
