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Sample GSM317905 Query DataSets for GSM317905
Status Public on Dec 22, 2008
Title WT 24 hr B
Sample type RNA
 
Channel 1
Source name A549, WT infection, 24 hr
Organism Homo sapiens
Characteristics A549 human respiratory epithelial cell line from lung carcinoma derived from 58 year old Caucasian male
Treatment protocol Sucrose purified wild-type, C(F170S), and P(C-) HPIV1 in Opti-MEM supplemented with 1.2 % Trypsin was inoculated at a multiplicity of infection of 5. 300 pg/mL (60 IU/mL) IFN-beta in Opti-MEM was used to treat A549 cells.
Growth protocol A549 cells were grown in F12 (Ham) media supplemented with 5% fetal bovine seruma, 4 mM L-glutamine, 0.1 mg/mL gentamicin. Cells were subcultured 1:3, twice a week
Extracted molecule total RNA
Extraction protocol Cellular homogenization, lysis, and RNA extraction was prepared using the QIAshredder and Qiagen RNeasy mini kits as per the manufacturer's protocols (Qiagen).
Label Cy5
Label protocol Sample labeling with Cy5 and Cy3 from 1 µg total RNA was performed using the Agilent 2-Color Low RNA Input Linear Amp Kit PLUS (Agilent Technologies) as per the manufacturer's protocols (Agilent).
 
Channel 2
Source name A549, Mock Infection, 24 hr
Organism Homo sapiens
Characteristics A549 human respiratory epithelial cell line from lung carcinoma derived from 58 year old Caucasian male
Treatment protocol Sucrose purified wild-type, C(F170S), and P(C-) HPIV1 in Opti-MEM supplemented with 1.2 % Trypsin was inoculated at a multiplicity of infection of 5. 300 pg/mL (60 IU/mL) IFN-beta in Opti-MEM was used to treat A549 cells.
Growth protocol A549 cells were grown in F12 (Ham) media supplemented with 5% fetal bovine seruma, 4 mM L-glutamine, 0.1 mg/mL gentamicin. Cells were subcultured 1:3, twice a week
Extracted molecule total RNA
Extraction protocol Cellular homogenization, lysis, and RNA extraction was prepared using the QIAshredder and Qiagen RNeasy mini kits as per the manufacturer's protocols (Qiagen).
Label Cy3
Label protocol Sample labeling with Cy5 and Cy3 from 1 µg total RNA was performed using the Agilent 2-Color Low RNA Input Linear Amp Kit PLUS (Agilent Technologies) as per the manufacturer's protocols (Agilent).
 
 
Hybridization protocol Samples were hybridized at 10 RPM at 65 °C for 18 hours as per the two-color microarray-based gene expression analysis version 5.5 protocol (Agilent Technologies).
Scan protocol Microarrays were scanned with an Agilent Microarray Scanner (Part Number G2565BA). Agilent Feature Extraction Software 9.5.1 was used for image acquisition. The single pass scan resolution was 5 micrometers, and extended dynamic range was activated.
Description Replicate B
Data processing Normalized values were derived from: 1) Averaging on-chip replicates; 2) Cy5/Cy3; 3) per chip normalization to the median
 
Submission date Sep 04, 2008
Last update date Dec 22, 2008
Contact name Jim Boonyaratanakornkit
E-mail(s) jim.boonyaratanakornkit@gmail.com
Phone 301-594-2589
Organization name NIH - NIAID
Department LID
Lab RVS
Street address 50 South Dr, Bldg 50, Rm 6513
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL6480
Series (1)
GSE12664 Analysis of wild-type and C mutant human HPIV1 and interferon beta treatment in human respiratory epithelial A549 cells

Data table header descriptions
ID_REF
VALUE Log base 10 (Cy5/Cy3)

Data table
ID_REF VALUE
A_23_P100001 0.12540472
A_23_P100011 0.48044127
A_23_P100022 -0.0699714
A_23_P100056 0.19702013
A_23_P100074 0.092941746
A_23_P100092 0.021566167
A_23_P100103 0.020109935
A_23_P100111 -0.026634416
A_23_P100127 0.021167442
A_23_P100133 -0.20724249
A_23_P100141 0.16292399
A_23_P100156 -0.064435594
A_23_P100177 -0.015870556
A_23_P100189 -0.056266014
A_23_P100196 0.23269925
A_23_P100203 0.09854064
A_23_P100220 -0.061864372
A_23_P100240 1.2334521
A_23_P10025 -0.5026571
A_23_P100263 -0.34513128

Total number of rows: 41000

Table truncated, full table size 974 Kbytes.




Supplementary file Size Download File type/resource
GSM317905.txt.gz 15.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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