|
| Status |
Public on Nov 05, 2016 |
| Title |
C.livia E3-E3.5 rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
retina
|
| Organism |
Columba livia |
| Characteristics |
tissue: retina
developmental stage: E3-E3.5
|
| Growth protocol |
Pigeon and chicken fertilized eggs were placed in a 37°C humidified incubator for the embryos to grow. Retinas were dissected in PBS, 1 to 6 whole retinas were collected in the proper volume of Trizol Reagent.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol Reagent (Life Technologies), following the manufacturer’s instructions
Stranded-mRNA libraries were prepared from 1 μg of total RNA using the The TruSeq Stranded mRNA Library Preparation Kit (Illumina), following the manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Read mapping was done using Tophat2/Bowtie2
Transcript abundances were calculated using cuffdiff from cufflinks package
Genome_build: WASHUC2 (chicken)
Genome_build: genome and transcript annotation reference files (assemblies from 2014-02-18) for pigeon were from (Giga)n database at gigadb.org
Supplementary_files_format_and_content: Two tab-delimited output files from cufflinks containing FPKM values for all transcripts in pigeon and chicken
|
| |
|
| Submission date |
Nov 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Michal Krawczyk |
| E-mail(s) |
mikrawczyk@gmail.com
|
| Organization name |
UCSD
|
| Department |
Ophthalmology
|
| Street address |
9500 Gilman Dr
|
| City |
La Jolla |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL22642 |
| Series (1) |
| GSE89541 |
Comparative transcriptomic profiling at E3-E3.5, E5-E5.5 and E8-E8.5 stages of retina development in pigeon and chicken |
|
| Relations |
| BioSample |
SAMN05981651 |
| SRA |
SRX2327551 |
