|
| Status |
Public on Oct 01, 2021 |
| Title |
OIR scrambled RNA 2 |
| Sample type |
SRA |
| |
|
| Source name |
Retina
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: Retina
age: P18
genotype: Wild type
disease state: oxygen-induced retinopathy
transfection: scrambled
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The enucleated rat eyes were harvested and stored in the RNAlater (Qiagen), and retinas were dissected immediately under the dissection microscope. Total RNA and miRNA were isolated from the dissected retina by using a miRNeasy mini kit (Qiagen, Hilden, Germany). One microgram of miRNA samples in triplicate was prepared as per the manufacturers’ instructions (Illumina Inc. San Diego, CA, USA). The libraries of cDNA from the biological samples in triplicate were sequenced by using an Illumina Hiseq-2500 RNA-seq platform as 50 bp single-end chemistry.
miRNA libraries were prepared for sequencing using a standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The quality of the raw reads were were assessed by the FASTQC (Andrews 2010) and assured that all read have phred score > 28.
The transcriptome reads were mapped to the Rattus norvegicus (rn6) refenerce genome retrieved from the iGenomes (obtained on 19th June 2017, https://support.illumina.com/sequencing/sequencing_software/igenome.html).
Differential gene and transcript expression analysis were done by using TopHat and Cufflinks (Trapnell et al. 2012).
Expression level and function analysis were done by using Cuffdiff (Zhang et al. 2014) statistical method and CummeRbund R statistical package (Trapnell et al. 2012).
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Oct 04, 2017 |
| Last update date |
Oct 01, 2021 |
| Contact name |
vikrant singh |
| E-mail(s) |
vikrantvicky.1987@gmail.com
|
| Organization name |
Royal college of Surgeons in Ireland
|
| Street address |
31 York Street
|
| City |
Dublin |
| State/province |
Ireland |
| ZIP/Postal code |
D02YN77 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE104588 |
Understanding the role of miRNA-143 (miR-143) in ischemia-induced retinopathy via RNA transcriptome profiling |
|
| Relations |
| BioSample |
SAMN07737152 |
| SRA |
SRX3242692 |
