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Sample GSM344965 Query DataSets for GSM344965
Status Public on Nov 26, 2008
Title WBC Holstein 3
Sample type RNA
 
Source name White blood cell, peripheral circulation
Organism Bos taurus
Characteristics Gender: female; Age: 6 months; Tissue: white blood cells; Disease state: heavy challenge with R.microplus
Treatment protocol N/A
Growth protocol White blood cells obtained via jugular venipuncture were collected into an EDTA vacuntainer; no growth or culture protocol was performed.
Extracted molecule total RNA
Extraction protocol 5 ml whole blood collected into EDTA vacutained was combined with 45 ml red blood cell lysis buffer and allowed to stand at room temperature for 10 min. Sample was spun at 250 g for 10 min to pellet cells and supernatant removed. The cell pellet containing a whole white blood cell extract was resuspended in 4 ml Trizol reagent (Invitrogen) and total RNA isolation carried out according to the manufacturer's instructions. DNase treatment was carried out with Turbo DNase (Ambion) according to the manufacturer's instructions.
Label biotin
Label protocol As per GeneChip expression manual, performed by the Australian Genome Research Facility
 
Hybridization protocol As per GeneChip expression manual, performed by the Australian Genome Research Facility
Scan protocol Agilent Microarray Scanner (Agilent Technologies) as per Affymetrix GeneChip manual
Description none
Data processing The data were analyzed with R/Bioconductor using RMA normalization. Additional parameters: background correction was convolution, quantile normalization and summarization with median polish.
 
Submission date Nov 24, 2008
Last update date Nov 25, 2008
Contact name Emily Kate Piper
E-mail(s) e.piper@uq.edu.au
Organization name University of Queensland
Department School of Veterinary Science
Street address Seddon Buildings (Bldg 82)
City Brisbane
ZIP/Postal code 4072
Country Australia
 
Platform ID GPL2112
Series (1)
GSE13725 Peripheral WBC from Brahman and Holstein-Friesian cattle infested with the cattle tick Rhipicephalus microplus

Data table header descriptions
ID_REF
VALUE RMA log2 signal intensity

Data table
ID_REF VALUE
AFFX-BioB-3_at 7.97795321523963
AFFX-BioB-5_at 7.95484980646107
AFFX-BioB-M_at 8.28028079589068
AFFX-BioC-3_at 7.82972411921584
AFFX-BioC-5_at 7.97085929757897
AFFX-BioDn-3_at 11.6688027557931
AFFX-BioDn-5_at 10.58354623234
AFFX-Bt-A00196-1_s_at 4.80869790800417
AFFX-Bt-AB076373-1_at 4.84554898495389
AFFX-Bt-actin-3_at 8.66764218533679
AFFX-Bt-actin-5_at 6.78931564573749
AFFX-Bt-actin-M_at 5.32668995602048
AFFX-Bt-AF292559-1_at 3.43315132668094
AFFX-Bt-AF292559-2_s_at 3.21797663735841
AFFX-Bt-AF292559-3_s_at 3.20999966334133
AFFX-Bt-AF292559-4_s_at 4.49836088635966
AFFX-Bt-AF292560-1_s_at 3.26085857011456
AFFX-Bt-AF298789-1_at 3.78520719738776
AFFX-Bt-AF323980-1_at 3.62841116063637
AFFX-Bt-AJ002682-1_s_at 4.14054928400352

Total number of rows: 24128

Table truncated, full table size 793 Kbytes.




Supplementary file Size Download File type/resource
GSM344965.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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