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Sample GSM317929 Query DataSets for GSM317929
Status Public on Dec 22, 2008
Title IFNB 6 hr C
Sample type RNA
 
Channel 1
Source name A549, IFN-beta, 6 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, 6 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 C
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 -0.15400423
A_23_P100011 -0.08253006
A_23_P100022 0.002372191
A_23_P100056 -0.044274546
A_23_P100074 0.1340126
A_23_P100092 0.10497607
A_23_P100103 -0.3390748
A_23_P100111 0.13871264
A_23_P100127 -0.024841182
A_23_P100133 0.043155998
A_23_P100141 -0.20365487
A_23_P100156 -0.02310746
A_23_P100177 -0.22195178
A_23_P100189 -0.28223217
A_23_P100196 -0.014415736
A_23_P100203 0.027051661
A_23_P100220 0.19179574
A_23_P100240 0.001987388
A_23_P10025 0.05345269
A_23_P100263 -0.16533381

Total number of rows: 41000

Table truncated, full table size 971 Kbytes.




Supplementary file Size Download File type/resource
GSM317929.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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