|
| Status |
Public on Oct 09, 2014 |
| Title |
shGFP_r1 |
| Sample type |
RNA |
| |
|
| Source name |
hESC
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
cell line: H9
genotype/variation: shRNA against GFP
|
| Treatment protocol |
Human embryonic stem cells (hESCs) were genetically marked with LTR7-GFP followed by sorting by FACS, in order to collect GFP(high), GFP(+) and GFP(low) cells. HESCs were transfected with shRNA against GFP, LBP9 and HERVH, respectively.
|
| Growth protocol |
Human embryonic stem cells (hESCs) were maintained on plates coated with Matrigel in hESC medium (knockout DMEM, 20% knockout serum supplement, 1 mM L-Glutamine, 1% nonessential amino acids, 0.1 mM 2-Mercaptoethanol, 10 ng/ml bFGF and primocin) with mitomycin-C treated mouse embryo fibroblasts (MEFs).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from ~3x10E6 cells using the RNeasy Plus kit from Qiagen followed by the TURBO DNA-free™ DNase Treatment, according to the manufacturer's instructions. Quality control was performed with Agilent Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled cRNA samples for hybridization on Illumina Human Sentrix-12 BeadChip arrays (Illumina, Inc.) were prepared according to Illumina's recommended sample labeling procedure
|
| |
|
| Hybridization protocol |
Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides.
|
| Scan protocol |
Microarray scanning was done using an iScan array scanner.
|
| Description |
shGFP_r1
|
| Data processing |
Intensities were extracted as data by BeadArray package which was processed using variance-stabilizing transformation (VST) by lumi package in R.
robust spline normalization (RSN) which combines the features of the quantile and loess normalization.
|
| |
|
| Submission date |
Feb 06, 2014 |
| Last update date |
Oct 09, 2014 |
| Contact name |
Gangcai Xie |
| Organization name |
Nantong University
|
| Department |
Medical school
|
| Lab |
Gangcai Xie Lab
|
| Street address |
Number 9, Se Yuan Road
|
| City |
Nantong |
| State/province |
Jiangsu |
| ZIP/Postal code |
226019 |
| Country |
China |
| |
|
| Platform ID |
GPL10558 |
| Series (2) |
| GSE54725 |
Repeat elements study in pluripotent stem cells [expression array] |
| GSE54726 |
Repeat elements study in pluripotent stem cells |
|
