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Sample GSM304356 Query DataSets for GSM304356
Status Public on Aug 26, 2008
Title Chip on chip e1a (IP infected vs INP infected) 6 h post infection
Sample type genomic
 
Channel 1
Source name IP infected IMR90 fibroblasts
Organism Homo sapiens
Characteristics IP infected IMR90 fibroblasts
Extracted molecule genomic DNA
Extraction protocol 2x107 IMR90 lung fibroblasts were grown on 10 cm dishes to confluence. After 24 h, the cells were incubated with mock- or the dl1500 adenovirus for 1 h in low serum media (2%). At the indicated times post infection (p.i.), formaldehyde was added for 10 min at 37°C. After PBS washing, cross-linked cells were scraped from the plates and washed with 1 ml of PBS containing protease inhibitors (Roche). Cells were resuspended in 400 µl of Lysis buffer and incubated for 10 min on ice and immediately sonicated. 100 µl of the lysate (corresponding to 5x106 cells) were used for immunoprecipitation with a given antibody (listed in table S1); 10 µl of the lysate was used as input. After overnight reversal of crosslinking at 65°C, samples were treated with RNase A for 30 min at 37°C and subsequently purified using the Qiagen Qiaquick PCR purification Kit. 10 ng of each IP and INP DNA were amplified using the WGA Kit (Sigma)(3).
Label cy5
Label protocol 2 μg of amplified material were labeled with Cy3 or Cy5 (PerkinElmer) using the Bioprime Labeling Kit (Invitrogen). DNA was mixed with 35 µl of random priming solution (Invitrogen Bioprime Kit) to a final volume of 75 µl, boiled for 5 min and quickly cooled in an ice-water bath for 5 min. The labeling reaction was completed with 60U Klenow, dNTPs (0.12 mM dATP, dGTP and dTTP and 0.06 mM dCTP), 1.28 mM Cy3 and Cy5 for input and IP (or IP from mock and IP from dl1500-infected cells) respectively, and incubated for 3h at 37°C. The labeled DNA was purified using Qiagen Qiaquick PCR purification Kit and the incorporation was measured with Nanodrop.
 
Channel 2
Source name INP infected IMR90 fibroblasts
Organism Homo sapiens
Characteristics INP infected IMR90 fibroblasts
Extracted molecule genomic DNA
Extraction protocol 2x107 IMR90 lung fibroblasts were grown on 10 cm dishes to confluence. After 24 h, the cells were incubated with mock- or the dl1500 adenovirus for 1 h in low serum media (2%). At the indicated times post infection (p.i.), formaldehyde was added for 10 min at 37°C. After PBS washing, cross-linked cells were scraped from the plates and washed with 1 ml of PBS containing protease inhibitors (Roche). Cells were resuspended in 400 µl of Lysis buffer and incubated for 10 min on ice and immediately sonicated. 100 µl of the lysate (corresponding to 5x106 cells) were used for immunoprecipitation with a given antibody (listed in table S1); 10 µl of the lysate was used as input. After overnight reversal of crosslinking at 65°C, samples were treated with RNase A for 30 min at 37°C and subsequently purified using the Qiagen Qiaquick PCR purification Kit. 10 ng of each IP and INP DNA were amplified using the WGA Kit (Sigma)(3).
Label cy3
Label protocol 2 μg of amplified material were labeled with Cy3 or Cy5 (PerkinElmer) using the Bioprime Labeling Kit (Invitrogen). DNA was mixed with 35 µl of random priming solution (Invitrogen Bioprime Kit) to a final volume of 75 µl, boiled for 5 min and quickly cooled in an ice-water bath for 5 min. The labeling reaction was completed with 60U Klenow, dNTPs (0.12 mM dATP, dGTP and dTTP and 0.06 mM dCTP), 1.28 mM Cy3 and Cy5 for input and IP (or IP from mock and IP from dl1500-infected cells) respectively, and incubated for 3h at 37°C. The labeled DNA was purified using Qiagen Qiaquick PCR purification Kit and the incorporation was measured with Nanodrop.
 
 
Hybridization protocol Hybridization onto the Human Promoter array (Agilent-G4489A), washing, and scanning were carried out according to the manufacturer's instructions
Scan protocol The arrays were scanned using an Agilent DNA Microarray scanner.
Description Data extraction and analyses were carried out using the Agilent Feature Extraction software (version 9.1.3.1) and Chip Analytics software (version 1.2). Probe signals were extracted with the Agilent Feature extraction software, normalized with Lowess normalization using the Chip Analytics software
Data processing Each ChIP profile was normalized to generate mean value of zero and variance of one, since the assay accurately captures the relative enrichment of an IP across an array.
 
Submission date Jul 08, 2008
Last update date Aug 25, 2008
Contact name Siavash K Kurdistani
E-mail(s) Skurdistani@mednet.ucla.edu
Organization name UCLA
Department Biological Chemistry
Lab Kurdistani
Street address 615 Charles E Young Dr South
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL7032
Series (2)
GSE12045 Expression profiles and ChIP on chip genomewide experiments with dl1500 virus (expressing WT small e1a).
GSE12543 Profiles and ChIP on chip experiments with dl1500 virus (expressing WT small e1a), R2G and deltaCR2 mutant viruses

Data table header descriptions
ID_REF
VALUE z-scored natural log of the ratio (Infected/Mock)

Data table
ID_REF VALUE
1 -0.28554
2 0.127013
3 -0.436373
4
5 1.018737
6 0.525435
7
8
9 -0.747193
10 -0.459055
11 0.129108
12 0.51769
13
14
15 0.200345
16 0.222142
17 -0.374622
18 -0.025392
19 0.414053
20 -0.065617

Total number of rows: 220672

Table truncated, full table size 2934 Kbytes.




Supplementary file Size Download File type/resource
GSM304356_e1a_6h_exp1.tsv.gz 54.4 Mb (ftp)(http) TSV
Processed data included within Sample table

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