|
| Status |
Public on Aug 27, 2012 |
| Title |
Zebrafish retina with Id2aMM morpholino treatment, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Zebrafish retina with Id2aMM morpholino treatment, replicate 1
|
| Organism |
Danio rerio |
| Characteristics |
tissue: retina
genotype/variation: control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from dissected retinae at 48 hpf using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 microgram of total retinal RNA per condition to generate cDNA libraries by poly-A selection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ctrl1
|
| Data processing |
Filter out all reads with no-call (‘N’) and low complexity (reads without all 4 bases).
Take reads that both paired-end reads are passed the above condition.
Map to EnsEMBL cDNA sequence, then calculate RPK100M (read counts per kb per 100 million of reads)
Summarize mapped reads per each cDNA.
Determine differentially expressed genes with DESeq
Genome_build: EnsEMBL version 66 cDNA sequences
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, DESeq output for differentially expressed genes.
|
| |
|
| Submission date |
Jun 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Taejoon Kwon |
| E-mail(s) |
tkwon@unist.ac.kr
|
| Organization name |
Ulsan National Institute of Science and Technology
|
| Department |
Department of Biomedical Engineering
|
| Street address |
50 Unist-gil
|
| City |
Ulsan |
| ZIP/Postal code |
44919 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE38786 |
Id2a knockdown in zebrafish retina |
|
| Relations |
| SRA |
SRX155008 |
| BioSample |
SAMN01055226 |
