|
| Status |
Public on Jul 01, 2018 |
| Title |
Normoxia_RNASeq |
| Sample type |
SRA |
| |
|
| Source name |
lung tissue_normoxia
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: lung
strain: Sprague Dawley
gasping time: not screened for gasping
sample details: Control or normoxic male (designated as Con(M))
gender: male
|
| Treatment protocol |
Rats screened for gasping time (time taken for arrival of first gasp during acute hypobaric hypoxia exposure) and divided into designated groups of susceptible, normal and tolerant animals. After acclimatization of a week, all the groups were exposed to simulated acute hypobaric hypoxia in a decompression chamber for one hour at 9144 m and 24°C. Relative humidity was maintained at 40-50% with airflow around 2 L/min inside the chamber.
|
| Growth protocol |
Rats were reared on daily standard nutritional diet and sterile water, at a temperature of 24±2ºC with day and night routine cycles of 12 hours each under hygienic disease free conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from lung tissue samples of control, susceptible male, normal male, tolerant male and female rats using TriReagent and its quality control analysis by Agilent 2100 Bioanalyser
RNA libraries were prepared for sequencing using standard Illumina TruSeq SBS kit v5-GA protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Each spreadsheet of processed file contains genes differentially expressed in samples as compared to control male (as reference).
|
| Data processing |
Base calling by Illumina Casava1.8 software.
The raw RNA-seq Fastq files were trimmed by for quality assurance by running perl script of IlluQC.pl of NGSQC Toolkit_v.2.2.
All reads from the five sample libraries were mapped together onto the reference genome of rat using large gap read mapper from CLC Genomics Workbench 6.02 to extend annotations.
Reads from individual library samples were aligned using RNA-seq analysis tool of same workbench to this newly annotated genome.
The differential gene expression was analyzed using normalized expression values based on exon based model RPKM (reads per kilo base per million) (Mortazavi et al. 2008).
Kal’s test was carried out for calculating differential gene expression in terms of proportional fold change of quantile based normalized data and Benjamini and Hochberg (1995) method to calculate FDR corrected p-values to control false positives (record with FDR < 0.05 was considered as significant).
Genome_build: RGSC_3.4
Supplementary_files_format_and_content: Each .xlsx processed data file contains spreadsheets having list of differentially expressed genes with proportional fold change > 2 or <-2 and FDR value below 0.05. The information on location of each differentially expressed transcript is given by the chromosome number, start and end region. Each spreadsheet's name symbolises the DEGs in one sample compared to other. For example, Sus(M) vs Con(M) has gene differentially expressed in Susceptible male as compared to control male.
|
| |
|
| Submission date |
Oct 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Prakash Chand Sharma |
| E-mail(s) |
prof.pcsharma@gmail.com
|
| Phone |
+91-9899088818
|
| Organization name |
GGS indraprastha University
|
| Department |
University School of Biotechnology
|
| Lab |
Genomics
|
| Street address |
Sector 16-C, Dwarka
|
| City |
New Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110078 |
| Country |
India |
| |
|
| Platform ID |
GPL10669 |
| Series (1) |
| GSE62688 |
Transcriptome profiling based study of early gene responses in susceptible and tolerant rat lung tissues during acute hypobaric hypoxia |
|
| Relations |
| BioSample |
SAMN03142773 |
| SRA |
SRX740862 |
