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Sample GSM1300331 Query DataSets for GSM1300331
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

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_52_P616356 6.665853496
A_52_P580582 6.885133668
A_52_P403405 6.71613912
A_52_P819156 6.735732615
A_51_P331831 12.96515562
A_51_P430630 7.010424417
A_52_P502357 6.664469555
A_52_P299964 6.839968978
A_51_P356389 6.708577314
A_52_P684402 7.797936211
A_51_P414208 6.669265507
A_51_P280918 7.519758334
A_52_P613688 8.03111563
A_52_P258194 6.752433337
A_52_P229271 6.782903226
A_52_P214630 6.831078874
A_52_P579519 6.768900363
A_52_P979997 6.663348254
A_52_P453864 6.698770737
A_52_P655842 6.786664031

Total number of rows: 41174

Table truncated, full table size 998 Kbytes.




Supplementary file Size Download File type/resource
GSM1300331_19_pp_38_14.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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