NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3616077 Query DataSets for GSM3616077
Status Public on Jan 31, 2021
Title Dd2clone1.10H_2.10E_0714
Sample type RNA
 
Source name Dd2
Organism Plasmodium falciparum
Characteristics strain: Dd2
time point (hours post invasion): 24
clone: 1.10H
sub-clone: 2.10E
culture date: 2014-07-14
feplicate: 1
Treatment protocol Culture were maintained under standard culture conditions.
Growth protocol The parasite strains HB3 and Dd2 were maintained in identical standard culture conditions in human red blood cells (Indiana Regional Blood Center, Indianapolis, Indiana) suspended in complete medium (CM) containing RPMI 1640 with L-glutamine (Invitrogen Corp.), 50 mg/L hypoxanthine (Sigma-Aldrich), 25 mM HEPES (Cal Biochem), 0.5% Albumax II (Invitrogen Corp.), 10 mg/L gentamicin (Invitrogen Corp.) and 0.225% NaHCO3 (Biosource) at 5% hematocrit. Cultures were grown separately in sealed flasks at 37˚C under an atmosphere of 5% CO2, 5% O2, and 90% N2. Replicated cultures were thawed and triple sorbitol synchronized. Total RNA was collected at 24 hours post invasion (hpi).
Extracted molecule total RNA
Extraction protocol RNA was extracted using TriZol reagent (Invitrogen, Carlsbad, CA) and the quality and quantity determined by NanoDrop (NanoDrop Technologies). 300ng of RNA was used as starting material for cDNA synthesis using the Sigma WTA2 whole transcriptome amplification kit (Sigma Aldrich, St Louis, MO).
Label Cy3
Label protocol 1µg of cDNA was labeled with Cy3 dye using 65% AT rich pre-labeled random hexamers as primers for cDNA synthesis by Klenow fragment of DNA polymerase I.
 
Hybridization protocol Cy3 labeled cDNA was allowed to hybridize for 17 h to a custom Agilent microarray (GPL22280) at 65°C at 10 rpm
Scan protocol The microarray image was taken using a 2 μM scanner and probe intensity values were obtained using Agilent Feature Extraction software.
Data processing Probe intensities for all samples were quantile normalized. Samples were visualized using Principle Component Analysis. Transcript expression levels were summarized for each gene by averaging the processed signal intensity of all the probes across its exons.
 
Submission date Feb 21, 2019
Last update date Feb 01, 2021
Contact name Michael T Ferdig
E-mail(s) ferdig.1@nd.edu
Organization name University of Notre Dame
Department Biological Sciences
Lab Ferdig lab
Street address 100 Galvin Life Sciences Center
City Notre Dame
State/province IN
ZIP/Postal code 46556
Country USA
 
Platform ID GPL22280
Series (1)
GSE126876 Sources of Transcription Variation in Plasmodium falciparum

Data table header descriptions
ID_REF
VALUE quantile normalized signal

Data table
ID_REF VALUE
PF3D7_0100100 675.83482
PF3D7_0100200 133.55982
PF3D7_0100300 3917.41181
PF3D7_0100600 16058.40078
PF3D7_0100700 11373.50391
PF3D7_0100800 1436.24271
PF3D7_0100900 4818.125
PF3D7_0101000 4387.81875
PF3D7_0101300 361.94464
PF3D7_0101500 442.21875
PF3D7_0101600 2375.49766
PF3D7_0101800 1587.55223
PF3D7_0101900 5190.50052
PF3D7_0102000 714.25234
PF3D7_0102100 1762.99716
PF3D7_0102200 1185.43776
PF3D7_0102300 1173.83047
PF3D7_0102400 351.5375
PF3D7_0102500 807.17917
PF3D7_0102600 2001.22857

Total number of rows: 5440

Table truncated, full table size 129 Kbytes.




Supplementary file Size Download File type/resource
GSM3616077_Dd2clone1.10H_2.10E_0714.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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