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| Status |
Public on Nov 16, 2020 |
| Title |
4hrs_T4 |
| Sample type |
SRA |
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| Source name |
Retina
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| Organism |
Gallus gallus |
| Characteristics |
tissue: Retina
breed: White Leghorn
Sex: Male
treatment: FDM + TPMPA injection, replicate 4
age: Post-hatch day 7
timepoint: 4 hours
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| Treatment protocol |
Male chicks were raised for 6 days under a 12 hours day/night light cycle. On day 7, chicks were randomly assigned to seven groups (age-matched untreated, FDM, FDM + atropine, FDM + pirenzepine, FDM + ADTN, FDM + TPMPA or recovery from FDM). Following 4 or 24 hours after diffuser attachment and/or intravitreal injection, retinae were collected, total RNA extracted and libraries prepared. For the 24-hour timepoint, a repeat injection was given 4 hours prior to collection. For recovery from FDM, chicks wore translucent diffusers for a period of 3 days to induce myopia before removing the device and collecting the retina 4 or 24 hours later.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the retina using the Trizol/chloroform protocol. RNA quality and quantity was assessed on a 2100 Bioanalyser. All samples had an RNA Integrity Number (RIN) greater than 7.0.
Libraries were prepared using the Ultra Directional RNA Library Kit for Illumina following the manufacturer's instructions. Libraries were validated on a 2100 Bioanalyser. Libraries were normalised to 4 ng/µL in 0.1x TE, pooled and sequenced at the Ramaciotti Centre for Genomics (UNSW, Sydney, Australia) on an Illumina NextSeq 500 platform (paired-end, 75 cycles).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were adaptor stripped using Trimmomatic software (v0.36).
Reads were mapped to the chick genome (GalGal5) using HISAT2 (v2.1).
Counts for ENSEMBL transcripts were obtained using analyzeRNA.pl, script from HOMER package.
Differential gene expression was analysed using EdgeR/limma with sample batch as blocking factor (Bioconductor release 3.6).
Genome_build: GalGal5
Supplementary_files_format_and_content: The CSV file was generated using the data processing steps described above. The table contains raw counts per sample, per condition, per timepoint.
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| Submission date |
Nov 15, 2020 |
| Last update date |
Nov 16, 2020 |
| Contact name |
Regan Ashby |
| E-mail(s) |
regan.ashby@canberra.edu.au
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| Phone |
+61262012088
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| Organization name |
University of Canberra
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| Department |
Faculty of Science and Technology
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| Street address |
University Drive, Bruce
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| City |
Canberra |
| State/province |
ACT |
| ZIP/Postal code |
2617 |
| Country |
Australia |
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| Platform ID |
GPL19787 |
| Series (1) |
| GSE161497 |
Gene expression across 4 and 24 hours of growth modulating paradigms in chicks |
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| Relations |
| BioSample |
SAMN16803193 |
| SRA |
SRX9510363 |
| 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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