|
| Status |
Public on Aug 28, 2015 |
| Title |
Control-1: invitro rings |
| Sample type |
RNA |
| |
|
| Source name |
P.falciparum invitro ring stages
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Red blood cells
agent: Plasmodium falciparum 3D7
|
| Treatment protocol |
Whole blood samples from malaria infected patients were collected into PAX gene blood RNA tubes for RNA extraction
|
| Growth protocol |
3D7 strain of Plasmodium falciparum was maintained in continuous culture and synchronized to ring stages using sorbitol and collected into PAX gene blood RNA tubes for RNA extraction 3D7 strain of Plasmodium falciparum was maintained in continuous culture and synchronized to ring stages using sorbitol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was isolated using PAXgene blood RNA kit according to manufacturer’s instructions
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared and purified using RNA binding beads according to the standard Affymetrix protocol from 500ng of total RNA (3' IVT express kit, affymetrix).
|
| |
|
| Hybridization protocol |
Labeled cRNA was fragmented for 35min at 94C according to 49/64 array format and hybridized on Plasmodium/Anopheles Genome Array for 16h at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using Affymetrix gene chip scanner 3000 using GCOS version 1.4 (FS450_0004)
|
| Description |
Gene expression data from in vitro ring stages
|
| Data processing |
First the probe level raw data (CEL files) from HP and LP group of samples were read separately for each sample and only the probes and the corresponding expression data of plasmodium Falciparum (PF) were selected for normalization using in house R and Perl scripts. Then the normalization of the data was done using widely used normalization technique, RMA ( Robust Multi-Array Average), an algorithm used to create an expression matrix from Affymetrix data using R/Bioconductor Affy library.Then using the limma package of R/Bioconductor and with threshold setting of 1.5 and 0.05 on fold change(FC) and p value respectively, the differentially expressed genes were obtained.
|
| |
|
| Submission date |
Aug 27, 2015 |
| Last update date |
Aug 28, 2015 |
| Contact name |
Sanjeev Kumar |
| E-mail(s) |
sanjeev@biocosls.in
|
| Organization name |
BioCOS Life Sciences Pvt Ltd
|
| Department |
R&D
|
| Lab |
R&D Bioinformatics
|
| Street address |
526/A,19th Main,3-sect,Ganesh Complex (2nd Floor) HSR Layout
|
| City |
Bangalore |
| State/province |
Karnataka |
| ZIP/Postal code |
560102 |
| Country |
India |
| |
|
| Platform ID |
GPL1321 |
| Series (2) |
| GSE72447 |
Interactions of PfETRAMP14.1 with PfEMP1 and EXP-2 at the parasitophorous vacuolar membrane (PVM) of human malaria parasite Plasmodium falciparum [LOW PARASITEMIA ANALYSIS] |
| GSE72448 |
Interactions of PfETRAMP14.1 with PfEMP1 and EXP-2 at the parasitophorous vacuolar membrane (PVM) of human malaria parasite Plasmodium falciparum |
|
| Relations |
| Reanalysis of |
GSM1862800 |
