|
| Status |
Public on Sep 13, 2016 |
| Title |
Fibroblast Day zero, Experiment 2 |
| Sample type |
RNA |
| |
|
| Source name |
adult fibroblasts, Coriell Institute, Cat # AG07714, treated as described
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: adult fibroblasts
cell line: AG07714
sample type: Fibroblasts passaged 2-3 days prior to day 0 and then harvested on day zero
|
| Biomaterial provider |
Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=AG07714
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared as described in the RNeasy Mini Kit (Qiagen) with on-column DNase I digestion. RNA quality was assessed by Nanodrop-1000 spectrometer for OD260/280 and OD260/230 ratio and Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
500 ng total RNA from each sample was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion, Austin, TX) as described in the instruction manual.
|
| |
|
| Hybridization protocol |
For array assay, 750 ng biotin-labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16-20 hours. After hybridization, the hybridization cartridge was disassembled and the array was washed with buffer at 55C and blocked at room temperature. Bound biotinylated cRNA was stained with streptavidin-Cy3 and then washed. Illumina HumanHT-12 V4.0 expression beadchips were used for all analyses in this series.
|
| Scan protocol |
Fluorescent signals were obtained by scanning with the iScan System.
|
| Description |
Individual sample
|
| Data processing |
Data were extracted with Gene Expression Module 1.0.6 in GenomeStudio 1.0.2 and signal intensities from multiple chips comprising this single series were quantile normalized without background subtraction to obtain normalized data as deposited.
|
| |
|
| Submission date |
Feb 20, 2013 |
| Last update date |
Sep 13, 2016 |
| Contact name |
Elias Thomas Zambidis |
| Organization name |
Johns Hopkins School of Medicine
|
| Department |
Oncology
|
| Street address |
733 N. Broadway
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL10904 |
| Series (2) |
| GSE44425 |
Global gene expression analysis of human embryonic stem cells, adult fibroblasts, and CD34+ cord blood (CB) cells before, during, and after generation of stromal primed and non-stromal primed episomal induction of pluripotency |
| GSE44430 |
Comprehensive microarray analysis of reprogramming fidelity in a library of non-integrated induced pluripotent stem cell lines prepared with various derivation methods |
|
