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Sample GSM1900135 Query DataSets for GSM1900135
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

Supplementary file Size Download File type/resource
GSM1900135_GCM90SH.txt.gz 111.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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