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Sample GSM317931 Query DataSets for GSM317931
Status Public on Dec 22, 2008
Title IFNB 24 hr B
Sample type RNA
 
Channel 1
Source name A549, IFN-beta, 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 Treatment, 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 -0.098841615
A_23_P100011 -0.30622727
A_23_P100022 0.27186233
A_23_P100056 -0.05123929
A_23_P100074 0.121447116
A_23_P100092 0.36580867
A_23_P100103 -0.251138
A_23_P100111 -0.10017845
A_23_P100127 0.002112064
A_23_P100133 3.01E-04
A_23_P100141 -0.42875442
A_23_P100156 0.049880914
A_23_P100177 -0.5200144
A_23_P100189 -0.06714092
A_23_P100196 0.03634084
A_23_P100203 -0.080056265
A_23_P100220 -0.1461275
A_23_P100240 -0.37955764
A_23_P10025 0.21309645
A_23_P100263 0.14524963

Total number of rows: 41000

Table truncated, full table size 968 Kbytes.




Supplementary file Size Download File type/resource
GSM317931.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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