|
| Status |
Public on Nov 24, 2008 |
| Title |
MEFF total RNA MS63 |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
total RNA from MEFF cells
|
| Organism |
Mus musculus |
| Characteristics |
Genotype: Thp/+
Age: cell line
Tissue: embryo
Strain: FVBN
Antibody: none
Type: ds cDNA from total RNA
|
| Treatment protocol |
MEFF and MEFB1 are spontaneously immortalized 12.5dpc mouse embryo fibroblast cells. The 93Mb long Chr.17 sequence in the two cell lines is identical with the exception of reciprocal Thp deletions on the paternal and maternal chromosome. The Thp deletion spans at least 4,6Mbp spanning the region between the genes T and Sod2 (8,6Mbp-13,2Mbp Mouse July 2007 mm9) and contains the 400kb Igf2r imprinted gene cluster (Regha et al., 2007).
|
| Growth protocol |
MEF cell lines were cultured according to standard protocols
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted and DNase1 trated according to standard protocols. Double stranded cDNA (ds cDNA) was prepared according to standard protocols (Regha et al., 2007 PMID: 17679087).
|
| Label |
Cy3
|
| Label protocol |
Samples were labeled and hybridized by Nimblegen Iceland (http://www.nimblegen.com).
|
| |
|
| Channel 2 |
| Source name |
Input DNA from Thp/+ MEF cells
|
| Organism |
Mus musculus |
| Characteristics |
Genotype: Thp/+
Age: cell line
Tissue: embryo
Strain: FVBN
Antibody: none
Type: sonicated genomic DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
see chanel 1
|
| Label |
Cy5
|
| Label protocol |
Samples were T7 amplified as published (Regha et al., 2007 PMID: 17679087) and labeled by Nimblegen Iceland (http://www.nimblegen.com).
|
| |
|
| |
| Hybridization protocol |
samples were hybridized by Nimblegen Iceland
|
| Scan protocol |
Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).
|
| Description |
RNA-chip MEF cells total RNA
|
| Data processing |
TUKEY NORMALISED log2 (ChIP/Input DNA) ratio
|
| |
|
| Submission date |
May 05, 2008 |
| Last update date |
Nov 24, 2008 |
| Contact name |
Florian M Pauler |
| E-mail(s) |
florian.pauler@univie.ac.at
|
| Phone |
+43 1 4277 54323
|
| Fax |
+43 1 42770 9546
|
| Organization name |
CeMM
|
| Lab |
Denise P Barlow
|
| Street address |
Dr Bohrgasse 9/4
|
| City |
Vienna |
| State/province |
Vienna |
| ZIP/Postal code |
A1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL6815 |
| Series (2) |
| GSE11337 |
RNA-chip from MEF cells |
| GSE11389 |
Mouse Chromosome 17 Mapping in Two MEF Cell Lines |
|
