|
| Status |
Public on Aug 01, 2014 |
| Title |
D10 ΔIDH/ΔKDH 0 hours post invasion |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
D10 ΔIDH/ΔKDH 0h RNA
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: D10 ΔIDH/ΔKDH
hours post invasion: 0
|
| Growth protocol |
P. faciparum wild-type D10 and ΔIDH/ΔKDH highly synchronized parasites were grown under standard culturing conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Starting at 0 hours post invasion, samples were harvested in Trizol for total RNA extraction every 6 hours for 48 hours.
|
| Label |
Cy5
|
| Label protocol |
Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).
|
| |
|
| Channel 2 |
| Source name |
3D7 Mixed Stage Reference Pool
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: 3D7
|
| Growth protocol |
P. faciparum wild-type D10 and ΔIDH/ΔKDH highly synchronized parasites were grown under standard culturing conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Starting at 0 hours post invasion, samples were harvested in Trizol for total RNA extraction every 6 hours for 48 hours.
|
| Label |
Cy3
|
| Label protocol |
Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).
|
| |
|
| |
| Hybridization protocol |
Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).
|
| Scan protocol |
Agilent G2505B Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).
|
| Data processing |
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and dye bias correction. Princeton University Microarray Database (https://puma.princeton.edu/) was utilized for log2 ratio calculation and data normalization.
|
| |
|
| Submission date |
Jul 02, 2014 |
| Last update date |
Aug 01, 2014 |
| Contact name |
Heather J Painter |
| E-mail(s) |
hjp117@psu.edu
|
| Phone |
8148673527
|
| Organization name |
Penn State University
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
Manuel Llinas
|
| Street address |
Millennium Science Center
|
| City |
University Park |
| State/province |
Pennsylvania |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL17880 |
| Series (1) |
| GSE59015 |
Gene expression analysis of a double knockout of TCA cycle enzymes IDH and KDH |
|
