|
| Status |
Public on May 17, 2021 |
| Title |
3D7-A Control, 40h Replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
3D7-A_2
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: 3D7-A
status: Control
age (hpi): 40
replicate: Biological replicate 2
|
| Treatment protocol |
All cultures (control and previously heat shock-adapted lines) were maintained at 37 ºC for the transcriptome characterization.
|
| Growth protocol |
Parasites were cultured under standard conditions in media containing Albumax II and no human serum, in a 5% CO2, 3% O2, 92% N2 atmosphere. Tight synchronization was achieved by Percoll or magnet purification of schizonts followed by sorbitol lysis 5 h later, to obtain a population of a defined age window of 0–5 h post- invasion. Parasites were cultured undisturbed for different periods of time (8, 16, 24, 32 and 40 h) before collecting in TRIzol for total RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol following manufacturer's instructions. For genomic DNA (gDNA) extraction, parasites were lysed with SDS and gDNA purified by double phenol/chloroform extraction and ethanol precipitation, followed by mild sonication.
|
| Label |
Cy5
|
| Label protocol |
Test sample, Cy5; reference pool, Cy3. Labeling was carried out as previously described [Bozdech Z et al Genome biol 2003, 4(2):R9].
|
| |
|
| Channel 2 |
| Source name |
3D7-A mixed stage Reference Pool
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: 3D7-A
age (hpi): Samples of synchronized cultures covering the whole asexual cycle.
|
| Treatment protocol |
All cultures (control and previously heat shock-adapted lines) were maintained at 37 ºC for the transcriptome characterization.
|
| Growth protocol |
Parasites were cultured under standard conditions in media containing Albumax II and no human serum, in a 5% CO2, 3% O2, 92% N2 atmosphere. Tight synchronization was achieved by Percoll or magnet purification of schizonts followed by sorbitol lysis 5 h later, to obtain a population of a defined age window of 0–5 h post- invasion. Parasites were cultured undisturbed for different periods of time (8, 16, 24, 32 and 40 h) before collecting in TRIzol for total RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol following manufacturer's instructions. For genomic DNA (gDNA) extraction, parasites were lysed with SDS and gDNA purified by double phenol/chloroform extraction and ethanol precipitation, followed by mild sonication.
|
| Label |
Cy3
|
| Label protocol |
Test sample, Cy5; reference pool, Cy3. Labeling was carried out as previously described [Bozdech Z et al Genome biol 2003, 4(2):R9].
|
| |
|
| |
| Hybridization protocol |
Microarray hybridizations were carried out using a MAUI hybridization system (BioMicro Systems) as previously described [Bozdech Z et al Genome biol 2003, 4(2):R9].
|
| Scan protocol |
Scanning was performed with a GenePix Pro 6.0 (Axon Instruments) as previously described [Bozdech Z et al Genome biol 2003, 4(2):R9].
|
| Description |
3D7-A-CTL_40h_repl2
|
| Data processing |
Microarray background for each channel (635 nm for Cy5 and 532 nm for Cy3) was calculated as the minimum between the median intensity of the 100 spots with lowest intensity and the median of the local background of all spots in the microarray. Spots with a signal in both channels lower than 1.5 fold times the background were eliminated. When a spot had intensity higher than 1.5 times the background in only one of the two channels, the other channel was assigned a value of 1.5 times the background of this channel, to avoid extreme ratio values. Background was subtracted before normalization. Log2(Cy5/Cy3) was normalized using LOESS.
|
| |
|
| Submission date |
Apr 27, 2020 |
| Last update date |
May 18, 2021 |
| Contact name |
Elisabet Tinto-Font |
| E-mail(s) |
elisabet.tinto@gmail.com
|
| Organization name |
ISGlobal
|
| Department |
Malaria
|
| Street address |
c/Rossello 153
|
| City |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11248 |
| Series (2) |
| GSE149393 |
Transcriptional alterations of P. falciparum 3D7-A heat shock-adapted vs control parasites. |
| GSE149394 |
Transcriptomic analysis of heat shock resistance in Plasmodium falciparum |
|
