|
| Status |
Public on Dec 16, 2014 |
| Title |
Mouse_19_+/+ |
| Sample type |
RNA |
| |
|
| Source name |
C/EBPb LIP wild type (+/+)_lymphoma
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: C/EBPb LIP wild type (+/+)
age (in month): 23
gender: female
tissue: lymphoma
|
| Treatment protocol |
C/EBPb LIP heterozygous (+/L) and wild type (+/+) mice were kept in a pathogen-free animal facility at least 25 months. Mice were checked twice a week for spontaneous lymphoma development. After dissection, one piece of the lymphoma was kept for histopathological analysis and the rest was snap-frozen and stored at - 80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using TriPure reagent and RNA cleaning step. Quality samples was checked using Agilent's Bioanalyzer.
|
| Label |
Cyanine-3 (Cy3)
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
19_pp_38_14
|
| Data processing |
Raw data was background corrected and normalized using quantile normalization (R/Bioconductor (1.8)).
|
| |
|
| Submission date |
Jan 02, 2014 |
| Last update date |
Dec 16, 2014 |
| Contact name |
Valerie Begay |
| E-mail(s) |
vbegay@mdc-berlin.de
|
| Organization name |
Max Delbrück Center
|
| Street address |
Robert-Rössle-Str. 10
|
| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE53770 |
Deregulation of the endogenous C/EBPβ LIP isoform predisposes to tumorigenesis |
|
