|
| Status |
Public on Sep 22, 2014 |
| Title |
PTB-depleted CSB deficient cell line, biological rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
PTB-depleted CSB deficient cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SV40 T-antigen transformed human fibroblasts derived from CS patient
transduced with: shPTB-expressing lentiviruses
|
| Treatment protocol |
Cells were transduced with either shCtrl- or shPTB-expressing lentiviruses, grew in fibroblast medium containing 0.2 μg ml-1 puromycin for three days before total RNA isolation.
|
| Growth protocol |
Transformed fibroblast cells were maintained in DMEM + 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy kit (Qiagen) as per the manufacturer's instructions.
|
| Label |
Cyanine 3
|
| Label protocol |
Double-stranded cDNA was synthesized using Nimblegen cDNA synthesis kit from 10-20 μg total RNA, up to 1 μg cDNA was labelled with Cy3 according to the standard Nimblegen protocol by using Nimblegen labeling kit.
|
| |
|
| Hybridization protocol |
Following labelling, 4ug of Cy3-cDNA were hybridized for 16 hr at 42ºC on Nimblegen 12 x 125K human expression array by using Nimblegen hybridization kit. The array was washed using Nimblegen washing buffers followed by drying on a microarray dryer.
|
| Scan protocol |
The array was scanned using NimbleGen MS 200 Microarray scanner.
|
| Description |
CS1AN_PTB2
|
| Data processing |
Data was analysed using Biocondutor 2.12 running on R3.0.0. Probe set expression measures were calculated using quantile normalisation of log2 transformed data.
|
| |
|
| Submission date |
May 29, 2014 |
| Last update date |
Sep 22, 2014 |
| Contact name |
Yuming Wang |
| E-mail(s) |
[email protected]
|
| Organization name |
Cancer Research UK
|
| Department |
Mechanisms of Transcription Laboratory
|
| Street address |
South Mimms
|
| City |
London |
| ZIP/Postal code |
EN6 3LD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18734 |
| Series (2) |
| GSE58069 |
Gene expression profile associated with PTB-mediated transdifferentiation of human fibroblast cells into neurons |
| GSE58071 |
Dysregulation of gene expression as the cause of Cockayne syndrome neurologic disease |
|
