|
| Status |
Public on Oct 01, 2015 |
| Title |
18hpi Unlabeled-2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
18 hpi 3D7attb::yFCU
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: 3D7attb::yFCU
time (hours post invasion): 18 hpi
sample type: Unlabeled RNA
|
| Treatment protocol |
50ml of standard culture was pulsed with 40uM 4-TU for 10 min prior to Trizol RNA extraction. This was repeated every hour 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
stages: Mixed stages
|
| Treatment protocol |
50ml of standard culture was pulsed with 40uM 4-TU for 10 min prior to Trizol RNA extraction. This was repeated every hour 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 Software (version 9.5.3.1).
|
| Description |
Sample name: 18 hpi U
|
| 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. 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 |
Mar 09, 2015 |
| Last update date |
Oct 01, 2015 |
| Contact name |
Heather J Painter |
| Phone |
8148673527
|
| Organization name |
Penn State University
|
| Department |
Molecular Biology & Biochemistry
|
| 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) |
| GSE66669 |
Plasmodium falciparum whole-genome real-time transcription and decay |
|
