|
| Status |
Public on Jan 01, 2015 |
| Title |
12h FCS |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
12h differentiated SFME cells in the presence of 10% FCS
|
| Organism |
Mus musculus |
| Characteristics |
cell type: serum free mouse embryo (SFME)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was isolated using NaCl/chloroform extraction
|
| Label |
Cy3
|
| Label protocol |
1 µg enriched and Input DNA was directly labeled by Klenow (nimblegen) random priming with Cy3 or Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).
|
| |
|
| Channel 2 |
| Source name |
mouse genomic DNA control
|
| Organism |
Mus musculus |
| Characteristics |
cell type: serum free mouse embryo (SFME)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was isolated using NaCl/chloroform extraction
|
| Label |
Cy5
|
| Label protocol |
1 µg enriched and Input DNA was directly labeled by Klenow (nimblegen) random priming with Cy3 or Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).
|
| |
|
| |
| Hybridization protocol |
The labeled Input and enriched DNA was precipitated with 11.5 µl 5M NaCl and 1 volume isopropanol, and hybridized in 14.4 µl HybridizationMix containing 2x Hybridization buffer, Hybridization Component A and alignment oligos together with 5.6 µl sample tracking control. Arrays were hybridized in Maui hybridization stations for 40-48h h at 42C, and then washed in wash-buffer I, II, III containing 0,1 % 1M DTT.Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf)
|
| Scan protocol |
Arrays were scanned on an nimblegen MS2000 scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).
|
| Data processing |
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.6 ChIP data extraction.
|
| |
|
| Submission date |
Feb 03, 2012 |
| Last update date |
Jan 01, 2015 |
| Contact name |
Andreas Keller |
| Organization name |
Saarland University
|
| Street address |
Building 60
|
| City |
Homburg |
| ZIP/Postal code |
69112 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10989 |
| Series (1) |
| GSE35523 |
Array CGH from mouse SFME cells and SFME cells differentiated with TGFB and FCS |
|
