|
| Status |
Public on Jan 25, 2023 |
| Title |
crb2a m289/m289 retina rep 5 [R56-crb05] |
| Sample type |
SRA |
| |
|
| Source name |
crb2a m289/m289 retina
|
| Organism |
Danio rerio |
| Characteristics |
genotype: crb2a (m289/m289)
hpf: 56
tissue: dorsal retina
|
| Growth protocol |
zebrafish were harvested at appropriate time points (hpf), retinal regions dissected
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen Rneasy FFPE kit and quantified
RNA-seq libraries were constructed using the SMARTer low input kit using standard protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimgalore
Reads were aligned to the genome and transcriptome using HISAT2 v2.2.1 using using standard paired end based parameters.
Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates
Count files were created using featurecounts (v2) and modelled using DESeq2 (v1.30.1)
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample
|
| |
|
| Submission date |
Jun 22, 2021 |
| Last update date |
Jan 25, 2023 |
| Contact name |
Mariya Moosajee |
| Organization name |
UCL
|
| Department |
Institute of Ophthalmology
|
| Street address |
11-43 Bath Street
|
| City |
London |
| ZIP/Postal code |
EC1V 9EL |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21741 |
| Series (1) |
| GSE178709 |
Transcriptome (RNA-seq) analysis of the retina of crumbs 2a (crb2a m289/m289) zebrafish model of Leber congenital amaurosis and retinitis pigmentosa. |
|
| Relations |
| BioSample |
SAMN19818051 |
| SRA |
SRX11200541 |
