NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1862808 Query DataSets for GSM1862808
Status Public on Aug 28, 2015
Title high parasitemia Patient sample 5
Sample type RNA
 
Source name P.falciparum peripheral blood ring stages
Organism Homo sapiens
Characteristics tissue: Red blood cells
agent: Plasmodium falciparum 3D7
Treatment protocol Whole blood samples from malaria infected patients were collected into PAX gene blood RNA tubes for RNA extraction
Growth protocol 3D7 strain of Plasmodium falciparum was maintained in continuous culture and synchronized to ring stages using sorbitol and collected into PAX gene blood RNA tubes for RNA extraction 3D7 strain of Plasmodium falciparum was maintained in continuous culture and synchronized to ring stages using sorbitol
Extracted molecule total RNA
Extraction protocol total RNA was isolated using PAXgene blood RNA kit according to manufacturer’s instructions
Label biotin
Label protocol Biotinylated cRNA were prepared and purified using RNA binding beads according to the standard Affymetrix protocol from 500ng of total RNA (3' IVT express kit, affymetrix).
 
Hybridization protocol Labeled cRNA was fragmented for 35min at 94C according to 49/64 array format and hybridized on Plasmodium/Anopheles Genome Array for 16h at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using Affymetrix gene chip scanner 3000 using GCOS version 1.4 (FS450_0004)
Description Gene expression data from pheripheral blood of severe malaria patient
Data processing First the probe level raw data (CEL files) from HP and LP group of samples were read separately for each sample and only the probes and the corresponding expression data of plasmodium Falciparum (PF) were selected for normalization using in house R and Perl scripts. Then the normalization of the data was done using widely used normalization technique, RMA ( Robust Multi-Array Average), an algorithm used to create an expression matrix from Affymetrix data using R/Bioconductor Affy library. Then using the limma package of R/Bioconductor and with threshold setting of 1.5 and 0.05 on fold change(FC) and p value respectively, the differentially expressed genes were obtained.
 
Submission date Aug 27, 2015
Last update date Aug 28, 2015
Contact name Sanjeev Kumar
E-mail(s) sanjeev@biocosls.in
Organization name BioCOS Life Sciences Pvt Ltd
Department R&D
Lab R&D Bioinformatics
Street address 526/A,19th Main,3-sect,Ganesh Complex (2nd Floor) HSR Layout
City Bangalore
State/province Karnataka
ZIP/Postal code 560102
Country India
 
Platform ID GPL1321
Series (2)
GSE72446 Interactions of PfETRAMP14.1 with PfEMP1 and EXP-2 at the parasitophorous vacuolar membrane (PVM) of human malaria parasite Plasmodium falciparum [HIGH PARASITEMIA ANALYSIS]
GSE72448 Interactions of PfETRAMP14.1 with PfEMP1 and EXP-2 at the parasitophorous vacuolar membrane (PVM) of human malaria parasite Plasmodium falciparum

Data table header descriptions
ID_REF
VALUE RMA normalized expression data of Plasmodium Falciparum probes only ( other probes from the chip was filtered out before normalization)

Data table
ID_REF VALUE
AB016617.1_RC_s_at 2.652048678
AF008978.1_RC_at 4.079320943
AF008978.1_x_at 2.502509381
AF008979.1_at 2.694076664
AF008979.1_RC_at 4.543228669
AF008979.1_x_at 3.616562577
AF008980.1_at 4.433566837
AF008980.1_RC_at 2.964962671
AF008980.1_RC_x_at 3.106405398
AF008980.1_x_at 4.559230969
AF008981.1_RC_at 4.176003211
AF008981.1_x_at 3.941537555
AF008982.1_at 3.538968777
AF008982.1_RC_at 3.938946716
AF008983.1_at 4.227971509
AF008983.1_x_at 3.974727432
AF008984.1_at 4.481019854
AF008984.1_RC_at 4.20131566
AF008985.1_at 3.066432309
AF008986.1_at 3.78042173

Total number of rows: 5407

Table truncated, full table size 158 Kbytes.




Supplementary file Size Download File type/resource
GSM1862808_Patient-MLR31b-HP5.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap