|
| Status |
Public on Sep 04, 2015 |
| Title |
3D7 Pfs 12h Unlabeled |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
12h 3D7::Pfs16-FCU Unlabeled RNA
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: 3D7::Pfs16-FCU
hours post invasion: 12
sample type: Total RNA
|
| Treatment protocol |
50ml of standard culture was pulsed with 40uM 4-TU for 12 hours prior to Trizol RNA extraction. This was repeated every 12 hours for 48 hours of intraerythrocytic development
|
| Growth protocol |
P. falciparum strain 3D7 was 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 hour 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
tag: Mixed stages
|
| Treatment protocol |
50ml of standard culture was pulsed with 40uM 4-TU for 12 hours prior to Trizol RNA extraction. This was repeated every 12 hours for 48 hours of intraerythrocytic development
|
| Growth protocol |
P. falciparum strain 3D7 was 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 hour 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 SoUnlabeledware (version 9.5.3.1).
|
| Data processing |
Agilent Feature Extraction SoUnlabeledware (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. Data normalization is based upon a novel methodology as follows: 1) filter out probes that are AGILENT_CONTROL, *rRNA*, NOT_UNIQUE, and NO_HIT 2) Determine log2 ratio (normalized based on intensity and background subtraction) on a set of 47 expression profiles for each sample type (Total, Unlabeled, and Label). 3) smooth 48 time-course profiles of each probe. 4) set negative values to a small positive value. 5) fit non-negative least squares (NNLS) for each probe to estimate how much of the unlabeled and labeled gene expression cntribute to the total gene expression. 6) compute fitted values for Total sample by adding estimated unlabeled and estimated labeled expression.
|
| |
|
| Submission date |
Sep 03, 2015 |
| Last update date |
Sep 04, 2015 |
| 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 |
GPL15130 |
| Series (1) |
| GSE72695 |
Capturing the dynamic RNA landscape of the malaria parasite P. falciparum |
|
