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Sample GSM139538 Query DataSets for GSM139538
Status Public on Oct 11, 2007
Title CBA brain naive
Sample type RNA
 
Source name CBA, brain, naive
Organism Mus musculus
Characteristics Strain: CBA/CaH
Gender: Female
Age: 6-7 weeks
Tissue: brain, perfused
Infection Status: naive
Biomaterial provider Animal Resources Centre, Australia
Treatment protocol Following sacrifice, mice were perfused with 20mL ice-cold PBS via the heart in order to remove blood and other non-adherent cells from the brain microvasculature. Brains were isolated, halved and preserved in either RNAlater (Qiagen, Doncaster, Australia).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from brain tissue using TRIzol reagent (Invitrogen, Mount Waverley, Australia), according to manufacturer’s instructions, and contaminants were removed by passing the RNA over RNeasy mini-columns with on-column DNase treatment (Qiagen). RNA 6000 Nano Assay Kits (Agilent Technologies, Forest Hill, Australia) were used to assess RNA quality and integrity on a Bioanalyzer 2100 (Agilent Technologies). Samples were included in the study based on 260:280nm absorbance readings. Equal quantities of six samples were pooled for microarray analysis.
Label R-Phycoerythrin
 
Hybridization protocol Pooled RNA samples were converted to cDNA and antisense cRNA, labelled and hybridized to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix, Surrey Hills, Australia) by the Australian Genome Research Facility (Parkville, Australia), according to Affymetrix protocols.
Scan protocol Arrays were scanned using the GeneChip Scanner 3000 (Affymetrix) and GeneChip Operating Software v1.1.1 (Affymetrix).
Description Normalisation and initial analyses were carried out in GeneSpring v7 (Agilent Technologies). Values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample. The data was filtered for genes flagged as present, which had at least an expression level of 50. Following this, a threshold of 2.5 fold up-regulation or down-regulation of genes was set.
Data processing Transformation algorithm used was MAS5.0
 
Submission date Oct 11, 2006
Last update date Aug 28, 2018
Contact name Christian Engwerda
E-mail(s) [email protected]
Organization name Queensland Institute of Medical Research
Lab Immunology and Infection
Street address 300 Herston Road, Herston
City Brisbane
State/province Queensland
ZIP/Postal code 4006
Country Australia
 
Platform ID GPL1261
Series (1)
GSE6019 Distinct pathways of pathogenesis in mice with experimental cerebral malaria following P. berghei ANKA infection.
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE Raw data
ABS_CALL Flagged as Present (P) or Absent (A)

Data table
ID_REF VALUE ABS_CALL
1415670_at 695.80 P
1415671_at 2440.00 P
1415672_at 1629.00 P
1415673_at 195.50 P
1415674_a_at 403.40 P
1415675_at 394.40 P
1415676_a_at 1525.00 P
1415677_at 481.30 P
1415678_at 1048.00 P
1415679_at 972.60 P
1415680_at 184.40 P
1415681_at 467.00 P
1415682_at 209.50 P
1415683_at 881.00 P
1415684_at 217.60 P
1415685_at 230.60 P
1415686_at 660.80 P
1415687_a_at 4910.00 P
1415688_at 999.30 P
1415689_s_at 154.00 P

Total number of rows: 45101

Table truncated, full table size 853 Kbytes.




Supplementary file Size Download File type/resource
GSM139538.CEL.gz 6.0 Mb (ftp)(http) CEL

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