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Sample GSM1868020 Query DataSets for GSM1868020
Status Public on Mar 01, 2016
Title GE GFP 0 day
Sample type RNA
Source name GE GFP 0 day
Organism Homo sapiens
Characteristics cell line: IMR90
transduction: Ad-GFP
condition: GFP
time: 0 day
Treatment protocol IMR90 cells were transduced with Ad-SOcMK or Ad-GFP. Adenoviruses were removed at 12 hrs post-transduction and cells were sampled at every 6 hrs.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from each sample using Qiagen RNeasy kit according to manufacturer’s protocol. 
Label Cy3
Label protocol The Agilent One-Color Quick Amp Labeling Kit is used to generate fluorescently labeled cRNA for one-color microarray hybridizations. Agilent RNA spike-in controls are combined with input total RNA samples (50 to 1000 ng). The polyadenylated fraction of the total RNA sample is primed with oligo dT/T7 RNA polymerase promoter oligonucleotide sequences and cDNA synthesis is accomplished through the addition of MMLV-RT. Following cDNA synthesis, T7 RNA polymerase and cyanine 3-CTP nucleotides are combined with the reaction mixture to simultaneously amplify the target material through the generation of cRNA and incorporate cyanine 3-CTP. Fluorescently labeled, cRNA molecules are purified from the reaction mixture using the Qiagen RNeasy mini kit. The concentration of the purified samples is determined using a NanoDrop ND-1000 spectrophotometer. 
Hybridization protocol Fluorescently labeled cRNA samples (825 ng each) were fragmented and combined with Agilent Hi-RPM Hybridization Buffer. Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers. Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization oven and were incubated at 65oC for 17 hours with a rotational speed of 10 rpm. Following incubation, the microarray slide was washed for 1 minute each in Gene Expression Wash Buffer 1 (6X SSPE, 0.005% N-lauroylsarcosine; room temperature) and Gene Expression Wash Buffer (0.06X SSPE, 0.005% N-lauroylsarcosine; room temperature) for 1 minute each. Microarray slides were briefly dipped in a solution of acetonitrile and dried.
Scan protocol Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution. The scanner can perform simultaneous detection of Cyanine-3 and Cyanine-5 signal on the hybridized slide. Data captured from the scanned microarray image is saved as a TIF file.
Description GFP_D_0
Data processing TIF files generated from the scanned microarray image are loaded into Agilent Feature Extraction Software version 10.5. The software automatically positions a grid and finds the centroid positions of each feature on the microarray. This information is used to perform calculations that include feature intensities, background measurements and statistical analyses. Data generated by the software is recorded as a tab-delimited text file.
Submission date Sep 02, 2015
Last update date Mar 01, 2016
Contact name Giovanni Coppola
Phone 310-794-4172
Organization name UCLA
Department Psychiatry and Neurology
Lab Neurogenetics
Street address 1524 Gonda, 695 Charles Young Drive South
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
Platform ID GPL13607
Series (1)
GSE72676 Co-expression networks in generation of induced pluripotent stem cells

Data table header descriptions
VALUE Normalized signal intensity

Data table
4 9.607397337
5 12.39162325
6 6.503987884
7 13.96393238
8 10.43233773
9 4.092176162
10 7.293010324
11 1.328348635
12 10.87423976
13 12.19769992
14 9.319525899
15 14.82348616
16 1.339380826
17 9.156203483
18 1.340015643
19 4.9759182
20 11.44070927
21 11.3080273
24 8.833460544
25 12.46825816

Total number of rows: 58717

Table truncated, full table size 1015 Kbytes.

Supplementary file Size Download File type/resource
GSM1868020_8248E15_252800414513_S01_GE1-v5.2_10_Apr08_2_2_3.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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