|
| Status |
Public on Aug 09, 2012 |
| Title |
nonviral Fetal fibroblast iPSC clone 6 |
| Sample type |
RNA |
| |
|
| Source name |
nonviral Fetal fibroblast iPSC clone 6, passage 14
|
| Organism |
Homo sapiens |
| Characteristics |
pasage: P14
cell type: nonviral Fetal fibroblast iPSC clone 6
sample type: non-integrated fetal fibroblast iPSC generated in the Zambidis laboratory
|
| 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 Nanodrp-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 V3.0 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 normalized without background subtraction to obtain non-normalized data. Signals for each gene were then log 2 transformed and mean subtracted across all conditions to obtain processed data.
|
| |
|
| Submission date |
Jan 11, 2012 |
| Last update date |
Aug 09, 2012 |
| 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 |
GPL6947 |
| Series (2) |
| GSE35028 |
Global gene expression analysis of pluripotent cell lines and corresponding starting donor source cells |
| GSE35029 |
Growth factor-activated stem cell circuits and stromal signals cooperatively accelerate iPSC reprogramming of lineage-committed myeloid progenitors |
|
