|
| Status |
Public on Mar 01, 2016 |
| Title |
GE iPS 2.5 day |
| Sample type |
RNA |
| |
|
| Source name |
GE iPS 2.5 day
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
transduction: Ad-SOcMK
condition: iPS
time: 2.5 days
|
| 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 |
iPS_D_2.5
|
| 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 |
| E-mail(s) |
gcoppola@ucla.edu
|
| 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 |
|
