|
| Status |
Public on Jan 01, 2017 |
| Title |
Control |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: whole embryo
treatment: DMSO
|
| Treatment protocol |
Embryos of stage HH8 were pretreated with thalidomide (40µg /ml) and spermine NONOate (10µM) separately and in combiantion. The embryos were collected on 6th day for isolation of total RNA
|
| Growth protocol |
The embryos were allowed to develop through stages in hatching incubator. At 6th day embryo was collected and processed for RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol reagent, Invitrogen Life Technologies. The total RNA samples was checked for quality using Nanodrop and 1% agarose gel. RNA samples, free of DNA and protein contamination was resuspended in in nuclease free water. 1ug of RNA sample for each stage was given for Next Generation Sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Alignment was performed using TopHat (v2.0.8) program to the Ensembl Release 75 gene model of chicken with default parameter settings
Differentially expressed genes were idenified using DESeq program
Genome_build: Galgal4 - Ensembl Release 75 database
|
| |
|
| Submission date |
May 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ravi Gupta |
| Organization name |
SciGenom Labs Pvt. Ltd.
|
| Department |
Bioinformatics
|
| Street address |
Plot no: 43A,SDF, 3rd floor, A Block,CSEZ, Kakkanad
|
| City |
Cochin |
| State/province |
Kerala |
| ZIP/Postal code |
682037 |
| Country |
India |
| |
|
| Platform ID |
GPL19005 |
| Series (1) |
| GSE69159 |
Modulation effects of nitric oxide on thalidomide treated chicken embryo transcriptome |
|
| Relations |
| BioSample |
SAMN03729542 |
| SRA |
SRX1036606 |
