|
| Status |
Public on Mar 01, 2021 |
| Title |
OV006 |
| Sample type |
SRA |
| |
|
| Source name |
Cornea
|
| Organism |
Oryctolagus cuniculus |
| Characteristics |
strain: New Zealand White
exsposure: 4 weeks post exposure to sulfur mustard vapor
clinical status: Clinically non-impaired
|
| Treatment protocol |
Rabbit eyes were exposed to SM vapor. At 4w, corneal tissues from clinically impaired, clinically non-impaired and naïve eyes were processed for RNA-seq.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Corneas were removed, incubated in RNA later over night and RNA was harvested using Tri-reagent (Sigma). 1 ug of total RNA was used for the construction of sequencing libraries.
TruSeq RNA Sample Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Supp2_Differential expression non-impaired vs naïve.xls
Supp3_Differential expression impaired vs non-impaired.xls
Supp4_comparison analysis heatmap canonical pathways.jpg
|
| Data processing |
RTA (Illumina) for base calling
bcl2fastq2 (version 2.17) for converting BCL to fastq format
Tophat (version 2.1.0) for mapping, with with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10)
Cufflinks (version 2.0.2) with default settings for the relative abundance (aka expression level) of genes and splice isoforms
Deseq for testing differentially expressed genes under various conditions
Ingenuity Pathway Analysis (IPA) , Qiagen, for canonical pathway analysis and heatmap generation
Genome_build: Rabbit: OryCun2.0 (GCA_000003625.1)
Supplementary_files_format_and_content: excel files including expression values , fold change and p-value for each gene in the comparison analysis; jpeg file including a heatmap comparing canonical pathways between the different sample comparisons, generated by Qiagen Ingenuity Pathway Analysis (IPA)
|
| |
|
| Submission date |
Mar 01, 2019 |
| Last update date |
Mar 02, 2021 |
| Contact name |
Ofir Israeli |
| E-mail(s) |
ofiri@iibr.gov.il
|
| Organization name |
IIBR
|
| Street address |
R lerrer
|
| City |
Ness Ziona |
| ZIP/Postal code |
74100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL21255 |
| Series (1) |
| GSE127708 |
A comprehensive analysis of corneal mRNA levels during sulfur mustard induced ocular late pathology in the rabbit model using RNA sequencing |
|
| Relations |
| BioSample |
SAMN11041529 |
| SRA |
SRX5447499 |
