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Sample GSM710795 Query DataSets for GSM710795
Status Public on Jun 30, 2011
Title P. falciparum-thiostrepton-treated-1
Sample type RNA
 
Source name P. falciparum, treated
Organism Plasmodium falciparum
Characteristics treatment: Thiostrepton
Treatment protocol Triplicate 15 ml cultures containing synchronous, ring stage parasites at 5 % parasitaemia were treated with 2 uM thiostrepton in DMSO (or 1/2000 vol. DMSO for controls) for 24 hours.
Growth protocol Blood stage P. falciparum 3D7 was maintained in continuous culture in vitro at 37 ºC using the candle-jar method. Cultures were maintained in citrated human blood at 2 % hematocrit with complete culture media (RPMI 1640 + L-Glutamine (Gibco) with 5 % w/v AlbuMAX I (Invitrogen), 50 μg.ml-1 hypoxanthine, 25 mM HEPES (Gibco) and 25 μg.ml-1 gentamycin (Sigma), pH of 7.6). Parasitaemia was assessed by thin blood smears stained with Giemsa (Sigma). Percentage infection of red blood cells was determined by cell counts under an oil immersion light microscope. Synchronous parasites were obtained by the Stockholm sorbitol method on two consecutive life cycles
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol (Invitrogen) as described (Kyes, 2004). RNA concentration and purity were determined using a NanoDrop (Thermo) and RNA integrity was tested using an Agilent Bioanalyzer (Cambridge Genomic Services, Department of Pathology)
Label Biotin
Label protocol Microarray cRNA synthesis, hybridisation and plate-reading were conducted by Geneservice (Nottingham, UK).
 
Hybridization protocol Microarray cRNA synthesis, hybridisation and plate-reading were conducted by Geneservice (Nottingham, UK).
Scan protocol Microarray cRNA synthesis, hybridisation and plate-reading were conducted by Geneservice (Nottingham, UK).
Description Gene expression data from LD70 thiostrepton-treated Plasmodium falciparum
Data processing Raw CEL files were imported into Bioconductor (Gentleman et al., 2004) for data analysis. Microarrays were analysed for RNA degradation prior to normalisation. Non-Plasmodium probesets were removed using the altcdfenvs package (Gautier et al., 2004) and microarray data were normalised using GCRMA (Wu et al., 2004). Differential gene expression was analysed using Linear Models for Microarray Analysis (LIMMA) (Smyth, 2004).
 
Submission date Apr 19, 2011
Last update date Jun 30, 2011
Contact name Sarah Tarr
E-mail(s) s.tarr@ucl.ac.uk
Organization name UCL
Department ISMB
Street address Gower Street
City London
ZIP/Postal code WC1E 6BT
Country United Kingdom
 
Platform ID GPL1321
Series (1)
GSE28701 Transcript-level responses of Plasmodium falciparum to thiostrepton

Data table header descriptions
ID_REF
VALUE Log2 GCRMA signal

Data table
ID_REF VALUE
AB016617.1_RC_s_at 5.761126642
AF008978.1_RC_at 2.168984474
AF008978.1_x_at 2.153220817
AF008979.1_at 2.151332755
AF008979.1_RC_at 2.151332755
AF008979.1_x_at 2.192083764
AF008980.1_at 2.253200496
AF008980.1_RC_at 2.151332755
AF008980.1_RC_x_at 2.151332755
AF008980.1_x_at 2.153397824
AF008981.1_RC_at 2.151332755
AF008981.1_x_at 2.564574866
AF008982.1_at 2.154586416
AF008982.1_RC_at 2.151332755
AF008983.1_at 2.151332755
AF008983.1_x_at 2.151332755
AF008984.1_at 2.160322738
AF008984.1_RC_at 2.151332755
AF008985.1_at 2.151332755
AF008986.1_at 2.151332755

Total number of rows: 5407

Table truncated, full table size 158 Kbytes.




Supplementary file Size Download File type/resource
GSM710795.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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