|
| Status |
Public on May 21, 2018 |
| Title |
A234T1_E11G |
| Sample type |
SRA |
| |
|
| Source name |
E11 male gonads
|
| Organism |
Gallus gallus |
| Characteristics |
breed: JA57
tissue: Male gonads
developmental stage: E11
|
| Growth protocol |
Fertilized eggs incubated at 37oC at 60% humidity to desired date
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples are extracted via TRIzol reagent according to according to manufacturers’ instructions.
Strand-specific library was constructed following Illumina TruSeq stranded total RNA sample preparation kit according to manufacture's instruction
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
strand-specific
|
| Data processing |
Adapter trimmed RNAs are aligned to gga5 genome assembly using tophat2, with options: -G galGal5.refseq.gtf --library-type fr-firststrand
Reference guided sequence assembly on RNA-seq samples using Cufflinks (v2.2.1), with options: --GTF-guide galGal5.refseq.gtf --frag-bias-correct galGal5.fa --multi-read-correct --library-type fr-firststrand --max-mle-iterations 500 --no-effective-length-correction --min-isoform-fraction 0.4 --pre-mrna-fraction 0.4 --min-frags-per-transfrag 100 --min-intron-length 20 --max-multiread-fraction 0.3 --3-overhang-tolerance 0 --intron-overhang-tolerance 0
Cuffmerge assemble the Cufflinks results of each RNA-seq samples, with option: --min-isoform-fraction 0.7
Cuffnorm for gene and novel transcript expression calculation on the RNA-seq samples, with reference to Cuffmerge results, with options: --library-type fr-firststrand
Supplementary_files_format_and_content: Cuffnorm normalized transcript expressions, for RNA-seq samples
|
| |
|
| Submission date |
Dec 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shau-Ping Lin |
| E-mail(s) |
shaupinglin@ntu.edu.tw
|
| Organization name |
National Taiwan University
|
| Department |
Institute of Biotechnology
|
| Street address |
No. 81, Chang-Xing St.
|
| City |
Taipei City |
| ZIP/Postal code |
10672 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL16133 |
| Series (1) |
| GSE98005 |
Oxidation treated small RNA-seq for studying roles of chicken piRNAs in germ cell development |
|
| Relations |
| BioSample |
SAMN08129760 |
| SRA |
SRX3442475 |
