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Sample GSM1627646 Query DataSets for GSM1627646
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

Data table header descriptions
ID_REF
VALUE Total, Labeled, and Unlabeled values calculated based on the intensity of Total Cy5 channel normalized to Cy3 reference and the estimated contributions of Labeled Cy5 and Unlabeled Cy3 to calculated Total Cy5.

Data table
ID_REF VALUE
4 1093.435135
5 79.57305537
6 201.5053842
7 0
8 369.6944441
9 409.3402889
10 699.5076534
11 606.6038917
12 3673.638879
13 0
14 413.0134787
15 12.1088958
16 1569.374115
17 2894.341686
18 541.617019
19 903.0713265
20 182.702228
21 805.9911455
22 763.2684569
23 308.6014352

Total number of rows: 14499

Table truncated, full table size 233 Kbytes.




Supplementary file Size Download File type/resource
GSM1627646_LLIHP20120511_253723710031_S01_GE2-v5_95_Feb07_no_spikein_1_4.txt.gz 4.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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