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Sample GSM439423 Query DataSets for GSM439423
Status Public on Oct 12, 2010
Title Time 3 17X
Sample type RNA
 
Source name spleen, day 3 post-infection, non-lethal 17X strain
Organism Mus musculus
Characteristics strain: BALB/c
tissue: spleen
gender: female
age: 6-8 weeks
Growth protocol Parasites from either strain were injected IP into Balb/c mice and daily parasitemia was monitored by Giemsa staining.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Trizol reagent as described in (http://www.medsci.uu.se/klinfarm/arrayplatform/TRIzol_Method%20(2).pdf). The protocol includes lysis of red and white blood cells and DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 1.5 ug of Cy3- (specific activity >10.0 pmol Cy3/ug cRNA) and Cy5-labeled cRNA were fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (GPL2872) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the GenePix 4000 scanner.
Description Gene expression spleen after 3 days post-infection with the non-lethal P. yoelii 17X strain.
Cy3_D3
Data processing Bioconductor limma package, using background correction (normexp) and quantiles normalization between arrays for final values. Cy3 and Cy5 channels are normalized values as separate channels for every GPR file.
 
Submission date Aug 11, 2009
Last update date Oct 12, 2010
Contact name Susana Kalko
E-mail(s) kalko.susana@gmail.com
Organization name IDIBAPS
Department Bioinformatics Platform
Street address c/Rosello 153
City Barcelona
State/province BARCELONA
ZIP/Postal code 08036
Country Spain
 
Platform ID GPL2872
Series (1)
GSE17603 Time series of Balb/c spleen infected with Plasmodium yoelii non-lethal vs lethal strains

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
3 7.331226726
4 6.689672544
5 6.350914652
6 7.29587154
8 7.054404475
9 6.653457771
10 8.614491656
12 7.213841727
13 7.201009639
15 6.671481681
16 7.054404475
17 7.847862815
18 7.148418365
19 6.546137564
20 8.886372233
22 9.055123511
23 7.69013615
24 6.94953335
25 7.239809548
26 6.86693755

Total number of rows: 41534

Table truncated, full table size 716 Kbytes.




Supplementary file Size Download File type/resource
GSM439423_d3_251269423042_Cy3.gpr.gz 6.4 Mb (ftp)(http) GPR
Processed data included within Sample table

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