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Sample GSM1507358 Query DataSets for GSM1507358
Status Public on Sep 19, 2014
Title TEC-Media control biological replicate 4 technical replicate 2_Cy3
Sample type RNA
 
Source name Tracheal epithelial cell
Organism Gallus gallus
Characteristics gender: Female
age: 5 weeks
tissue: Trachea
Treatment protocol TECs were exposed to either 500 MOI live Mycoplasma gallisepticum Rlow or Rhigh or 5µg/mL LAMPs from either strain for 1.5 hours for microarray experiments.
Growth protocol Chicken tracheal epithelial cells were isolated from chicken trachea and cultured in ATE medium (described in manuscript) at 37C with 5% CO2 in a cell culture incubator for 96 hours. Mycoplasma gallisepticum strains were grown in Hayflicks media at 37C. All LAMPs were isolated using TX-114 phase seperation.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using a combination protocol of Trizol-Chloroform extraction followed by purification using Qiagen RNEasy Mini kit (Qiagen, Valencia, CA)
Label Cy3
Label protocol Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNA was prepared from 50 ng RNA using the Two-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 total cRNA (750 ng Cy3-labelled cRNA and 750 ng Cy-5-labelled) (specific activity >7 pmol Cy3/ug cRNA or >7 pmol Cy5/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) 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 4000B Laser Scanner using two color scan setting (Scan resolution 5um). PMT gains were adjusted to give equal ratio of Cy3 and Cy5 intensity while keeping saturated features to less than 1%.
Description R(low)3-4.gpr
Gene expression upon exposure to media control for 1.5 hr
Data processing The scanned images were analyzed with GenePix Pro 7 for feature extraction (Molecular Devices) using default parameters to obtain background subtracted Signal intensities for each channel. Background intensity was calculated as the mean value of the 5 closest negative control features. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Sep 18, 2014
Last update date Sep 19, 2014
Contact name Frank Zappulla
E-mail(s) frank.zappulla@engr.uconn.edu
Organization name University of Connecticut
Department Pathobiology
Street address 61 North Eagleville Road
City Storrs
State/province CT
ZIP/Postal code 06269
Country USA
 
Platform ID GPL15357
Series (1)
GSE61520 Mycoplasma gallisepticum Lipid Associated Membrane Proteins Up-regulate Inflammatory Genes in Chicken Tracheal Epithelial Cells via TLR-2 Ligation Through an NF-κB Dependent Pathway

Data table header descriptions
ID_REF
VALUE processed signal

Data table
ID_REF VALUE
(-)3xSLv1 0.120207965
(+)E1A_r60_1 0.6692753
(+)E1A_r60_3 -0.15595722
(+)E1A_r60_a104 0.06646633
(+)E1A_r60_a107 1.1684723
(+)E1A_r60_a135 1.2866516
(+)E1A_r60_a20 1.1590958
(+)E1A_r60_a22 -0.6155052
(+)E1A_r60_a97 -0.16012573
(+)E1A_r60_n11 1.3841953
(+)E1A_r60_n9 2.0550404
(+)eQC-39 0.044149876
(+)eQC-40 0.049760282
(+)eQC-41 0.2140007
(+)eQC-42 -0.18796986
A_87_P000014 1.7207524
A_87_P000029 -0.61701035
A_87_P000043 -0.06512819
A_87_P000046 0.47547865
A_87_P000062 -0.95799446

Total number of rows: 43663

Table truncated, full table size 1034 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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