|
| Status |
Public on Feb 11, 2020 |
| Title |
Time 16_Control_Rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
Nf54 attB parasites,Time 16, Rep 3
|
| Organism |
Plasmodium falciparum |
| Characteristics |
tissue: Blood-stage Nf54 attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit
time: Time 16
treatment: Control
slide id (array batch): 253723710162
replicate: Rep 3
|
| Treatment protocol |
Genetically engineered Plasmodium falciparum parasites (PfMev) were treated with azithromycin to disrupt the apicoplast. These apicoplast negative PfMev parasites were cultured as described in in the paper, at 2% hematocrit and supplemented with 50μM mevalonate.
|
| Growth protocol |
Blood-stage P. falciparum parasites were cultured in human erythrocytes at 2% hematocrit in CMA (Complete Medium with Albumax) containing RPMI 1640 medium with L-glutamine (USBiological Life Sciences), supplemented with 20mM HEPES, 0.2% sodium bicarbonate, 12.5μg/ml hypoxanthine, 0.5μM R-lipoic acid, 5g/L Albumax II (Life Technologies) and 25μg/mL gentamicin. Cultures were maintained in 25cm2 gassed flasks (94% N2, 3% O2, 3% CO2) and incubated at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each data point, RNA was extracted from 50 µL of packed RBC culture with Trizol Reagent and the PureLink Mini Kit (Invitrogen/Thermo Fisher Scientific). 1ml Trizol was added to each sample, followed by high-speed disruption in tubes containing Lysing Matrix D (MP Biomedical) in a FastPrep 120 Instrument at speed 6 for 20 seconds. Homogenates were subsequently processed according to the PureLink Mini Kit manufacturer’s (Invitrogen/Thermo Fisher Scientific) protocol, including on-column DNase treatment.
|
| Label |
Cy3
|
| Label protocol |
From 100 ng of total RNA, Cyanine-3 labeled cRNA was prepared using the Low Input Quick Amp Labeling Kit One-Color (Agilent).
|
| |
|
| Hybridization protocol |
The eight time course samples were hybridized (along with the manufacturer’s RNA spike-in controls) according to standard protocol to the 8 sectors of an Agilent 8x15K platform microarray (AMADID 037237) with separate microarray slides used for each biological replicate (in quadruplicate for each condition).
|
| Scan protocol |
Arrays were scanned with the Agilent G2600D SureScan microarray scanner using scan protocol AgilentHD_GX_1color. Agilent’s Feature Extraction Software was used to assign grids, provide raw image files per array, and generate QC metric reports from the microarray scan data.
|
| Description |
Gene Expression Data
|
| Data processing |
Txt files from Agilent’s Feature Extraction Software were transferred to Partek Genomics Suite software (v7.0). Within Partek, the gProcessedSignal was imported and the intensity values were normalized using Quantile Normalization and Log Tranformation Base 2.0 after import.
|
| |
|
| Submission date |
Aug 21, 2019 |
| Last update date |
Feb 11, 2020 |
| Contact name |
Anne E. Jedlicka |
| Organization name |
Johns Hopkins University, School of Public Health
|
| Department |
Molecular Microbiology and Immunology
|
| Lab |
Genomic Analysis and Sequencing Core
|
| Street address |
615 N. Wolfe street
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL27130 |
| Series (1) |
| GSE136169 |
A mevalonate bypass system facilitates elucidation of apicoplast biology in malaria parasites |
|
| Relations |
| Reanalyzed by |
GSM4055265 |
