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| Status |
Public on Sep 17, 2016 |
| Title |
LID73 |
| Sample type |
SRA |
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| Source name |
Retina, RPE, choroid
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| Organism |
Gallus gallus |
| Characteristics |
tissue: Retina, RPE, choroid
Sex: male
breed: Leghorn/New Hampshire
age: Post-hatch day 6
time-point: 1 day (post-lensing)
lens type: No Lens
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| Treatment protocol |
Male chicks (Leghorn/New Hampshire) were raised from post-hatch days 0-4 under a 12-hr day/night light cycle in groups of <25. In the middle of the light cycle on day 5, chicks were randomly assigned to a lens condition (+10 or -10 dioptres, or No Lens) and lenses (Polymethyl Methacrylate) attached to Velcro were fixed to the periocular feathers of the right eye. Following a further 1, 2, or 3 days with lenses attached, chicks were anaesthetized and right eye refraction and axial dimensions determined by retinoscopy and A-Scan ultrasonography. Chicks were euthanized and their right eyes were enucleated. The retina/RPE/choroid was immediately collected from the posterior eyecup and frozen in liquid nitrogen before being transferred to -80°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the retina/RPE/choroid using the miRNeasy Mini Kit (Qiagen) including DNase digestion. RNA quality and quantity was assessed on the 2100 Bioanalyzer. All samples had an RNA integrity number (RIN) of >8.3. RNA quantity was also assessed on the Qubit 2.0 Fluorometer.
Libraries were prepared using the TruSeq Stranded mRNA LS kit (Illumina) with dual indexing according to the manufacturer’s instructions. The generated libraries were assessed on the 2100 Bioanalyzer to ensure an average size distribution of approximately 280bps, then quantified on the Qubit 2.0 Fluorometer and by qPCR. Libraries were normalised to 10nM in Tris-HCl, pooled, and prepared for cluster generation on the Illumina cBot using the TruSeq SR Cluster Kit V3-cBot (Illumina) with denatured template DNA diluted to 7pM. The flow cell and sequencing reagents (TruSeq SBS Kit V3; Illumina) were loaded on the Illumina HiSeq 1500 and a dual-index, single-end, 100bp sequencing run performed.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
Read quality was assessed using FastQC
Adapter and low quality (Q-score <10) sequences removed using CutAdapt and Trimmomatic
Reads were mapped to the chick genome using Tophat2 and Bowtie2
The number of reads uniquely mapping to each gene was counted using existing gene models with HTSeq
Genome_build: GalGal4
Supplementary_files_format_and_content: The txt file was generated using the data processing steps described above. It is matrix table containing processed data for all samples (raw counts)
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| Submission date |
Feb 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Nina Riddell |
| E-mail(s) |
nina.riddell@gmail.com
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| Organization name |
La Trobe University
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| Department |
Psychology and Public Health
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| Lab |
Crewther Lab
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| Street address |
La Trobe University, Plenty Rd.
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| City |
Bundoora |
| State/province |
Victoria |
| ZIP/Postal code |
3086 |
| Country |
Australia |
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| Platform ID |
GPL21476 |
| Series (1) |
| GSE78042 |
Gene expression across 3 days of lens-induced myopia and hyperopia induction in chick |
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| Relations |
| SRA |
SRX1590682 |
| BioSample |
SAMN04502722 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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