|
| Status |
Public on Dec 07, 2016 |
| Title |
AGS Non-Targeting Control RNA treated biological replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
AGS cell line (Gastric adenocarcinoma)_control RNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: AGS
tissue: Stomach
cell type: gastric cancer
|
| Treatment protocol |
In AGS cells, anti-miR miR-25-3p inhibitor or non targeting control RNA was transfected with oligofectamine transfection reagent (invitrogen). AGS cells were transfected with miRNA inhibitor at 70 % confluency. 24 hrs after transfection, cells were transfected again with miRNA inhibitor or non targeting control RNA . After 48 hrs of first transfection, cells were harvested and total RNA was isolated.
|
| Growth protocol |
AGS cells were grown in DMEM (F12/HAM) media with 10% FBS and 2mM Glutamine. The cells were incubated at 37ºC with 5%CO2 and 95% humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy Mini Kit as per the instructions provided by the manufacturer.
|
| Label |
Biotin
|
| Label protocol |
Biotin was labelled to the single stranded cDNA fragments prepared from 500 ng of total RNA. The steps were followed as per the instructions in the user manuals of Ambion® WT Expression Kit, GeneChip® WT Terminal Labeling and Hybridization kit (Affymetrix).
|
| |
|
| Hybridization protocol |
The biotin labelled single stranded cDNA was hybridized with the probes on Human Gene 1.0 ST Array for 16 hrs at 45ºC using GeneChip Hybridization Oven 640. GeneChips were stained with Phycoerythrin and washed using GeneChip Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using GeneChip® Scanner 3000 7G system.
|
| Description |
mRNA profile of AGS cells treated with non targeting control RNA
|
| Data processing |
The CEL files were subjected to RMA normalization at exon level using Expression Console (EC) software of Affymetrix. The CHP files were analysed for differential gene expression in Transcriptome Analysis Console (TAC) software of Affymetrix.
|
| |
|
| Submission date |
Jul 08, 2016 |
| Last update date |
Dec 07, 2016 |
| Contact name |
Kumaresan Ganesan |
| E-mail(s) |
kumar@oncocellomics.org
|
| Organization name |
Madurai Kamaraj University
|
| Department |
Genetics
|
| Street address |
School of Biological Sciences,
|
| City |
Madurai |
| State/province |
Tamil Nadu |
| ZIP/Postal code |
625021 |
| Country |
India |
| |
|
| Platform ID |
GPL10739 |
| Series (1) |
| GSE84196 |
mRNA profiling in gastric cancer cell line AGS upon miR-25-3p silencing |
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