|
| Status |
Public on Nov 19, 2014 |
| Title |
RNA_T4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
TP4 Plasmodium falciparum in culture
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: T996
timepoint (hours post invasion): TP4=32hpi
|
| Growth protocol |
P. falciparum T996 strain was cultured following standard methods.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from each time point was isolated by trizol method.The chromatin immunoprecipitation assay was performed as described in Gupta AP et.al. 2013.
|
| Label |
Cy5
|
| Label protocol |
For expression analsysis, samples for individual time points (labeled with Cy5, red) were hybridized against a reference pool (labeled with Cy3, green) which consisted of a mixture of RNA from all the six time points in equal amounts. Amplified ChIP and input DNA were labeled with Cy5 and Cy3 respectively.
|
| |
|
| Channel 2 |
| Source name |
total RNA from pooled TP1-6
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: T996
control type: cDNA from pooled total RNA
|
| Growth protocol |
P. falciparum T996 strain was cultured following standard methods.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from each time point was isolated by trizol method.The chromatin immunoprecipitation assay was performed as described in Gupta AP et.al. 2013.
|
| Label |
Cy3
|
| Label protocol |
For expression analsysis, samples for individual time points (labeled with Cy5, red) were hybridized against a reference pool (labeled with Cy3, green) which consisted of a mixture of RNA from all the six time points in equal amounts. Amplified ChIP and input DNA were labeled with Cy5 and Cy3 respectively.
|
| |
|
| |
| Hybridization protocol |
The microarray hybridization was carried at 63.50 °C or 65.0 °C in an automated hybridization station (Maui, USA) for ChIP DNA or cDNA respectively as described previously in Bozdech Z et al., 2003.
|
| Scan protocol |
The microarrays were scanned using the GenePix scanner 400b and GenePix pro 6.0 software (Axon Laboratory).
|
| Data processing |
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed green signal. Limma Package of R was used.
|
| |
|
| Submission date |
May 16, 2014 |
| Last update date |
Nov 19, 2014 |
| Contact name |
Mark Stephen Featherstone |
| E-mail(s) |
msfeatherstone@gmail.com
|
| Organization name |
Nanyang Technological University
|
| Department |
School of Biological Sciences
|
| Lab |
03n-39
|
| Street address |
60, Nanyang Drive
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL11250 |
| Series (1) |
| GSE57748 |
Genome-wide RNA polymerase II recruitment study during the intraerythrocytic life cycle of Plasmodium falciparum. |
|
