|
| Status |
Public on Dec 20, 2018 |
| Title |
Control_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Control_rep1
|
| Organism |
Cicer arietinum |
| Characteristics |
agent: Control
leaves: 15 days leaves
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was perforemd by using Qiagen Rneasy mini kit following the manufacturer's recommendations.
|
| Label |
Cy3
|
| Label protocol |
The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.
|
| |
|
| Hybridization protocol |
600ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Genotypic designed Chickpea GXP_8X60K (AMADID: 037094). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65°C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327) and scanned using the Agilent Microarray Scanner (AgilentTechnologies, Part Number G2600D).
|
| Scan protocol |
Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).
|
| Data processing |
Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the quantile normalization method .Gene based analysis was performed.
|
| |
|
| Submission date |
Sep 12, 2016 |
| Last update date |
Dec 20, 2018 |
| Contact name |
Ashutosh Mani |
| E-mail(s) |
amani@mnnit.ac.in
|
| Phone |
9455354251
|
| Organization name |
MNNIT, Allahabad
|
| Street address |
Teliarganj
|
| City |
Allahabad |
| State/province |
U.P. |
| ZIP/Postal code |
211004 |
| Country |
India |
| |
|
| Platform ID |
GPL22423 |
| Series (1) |
| GSE86807 |
Genome expression profiling of Chick pea under Abiotic Stress |
|
