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| Status |
Public on Mar 14, 2016 |
| Title |
LungTumorNodule_mouse645_Kras37bpMarkerGenotype_A_homozygous_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
LungTumorNodule_Kras37bpMarkerGenotype_A_homozygous
|
| Organism |
Mus musculus |
| Characteristics |
strain background: A/J X C57BL/6
strain: offspring bred to the 4th generation (ABF4)
gender: male
age: 40 wks
number of lung tumors: 11
kras37bp marker genotype: A_homozygous
tissue: lung tumor nodule
batch: batch1
|
| Treatment protocol |
At 4 weeks of age, 143 male ABF4 mice were treated with a single intraperitoneal injection of urethane (1 g/kg body weight) according to a standard procedure for inducing the development of lung tumors (Shimkin, 1975).
|
| Growth protocol |
Mice were maintained at the animal facility of Fondazione IRCCS Istituto Nazionale dei Tumori. Animal experiments were authorized by the Institute Animal Experimentation Ethical Committee (CESA) in March 2012, according to the Italian law DL116/92), and performed in accordance to institutional guidelines
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from lung tumor specimens using RNeasy Midi Kit (Qiagen), purified with RNeasy MinElute Cleanup (Qiagen), and quantified by spectrophotometry (ND-1000 spectrophotometer, NanoDrop, Wilmington, DE, USA). RNA integrity was verified using the RNA 6000 Nano Assay Kit (Agilent Technologies, Palo Alto, CA, USA); the mean RIN value was 8.9 (SD = 0.8; range, 6.7 to 9.9).
|
| Label |
Cy3
|
| Label protocol |
Total RNA was amplified using the Low Input Quick Amp WT Labeling kit, according to the manufacturer’s instructions (Agilent Technologies, Santa Clara, USA). 100 ng of total RNA was reverse-transcribed into double-stranded cDNA, which was translated into cRNA in the presence of Cy3-dCTP and amplified by T7 RNA polymerase.
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| |
|
| Hybridization protocol |
Fluorescent dye-labeled cRNA was hybridized to SurePrint G3 Mouse Exon 4x180K arrays (Agilent); hybridization and washing were performed on Agilent’s microarray platform, according to standard protocols.
|
| Scan protocol |
Microarray images were acquired using an Agilent DNA microarray scanner.
|
| Description |
sample name: 645
|
| Data processing |
Raw data were generated using Agilent Feature Extraction software. Raw median probe intensities were pre-processed using the limma (Ritchie, 2015) package of the R/Bioconductor project. A batch effect was present as samples had been assayed in two different experiments (95 samples in batch 1 and 48 samples in batch 2). Thus, raw data from each batch of arrays were log2-transformed and normalized independently using quantile normalization. The ComBat method (Johnson, 2007), implemented in the sva R package (Leek, 2012), was then applied to remove the batch effect from normalized data. After ComBat correction expression data from replicated probes were summarized calculating the mean expression.
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| |
|
| Submission date |
Jul 22, 2015 |
| Last update date |
Mar 14, 2016 |
| Contact name |
Matteo Dugo |
| E-mail(s) |
dugo.matteo@hsr.it
|
| Organization name |
IRCCS Ospedale San Raffaele
|
| Department |
Department of Medical Oncology
|
| Street address |
via Olgettina 60
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL20726 |
| Series (1) |
| GSE71232 |
Expression quantitative trait loci (eQTL) analysis of mouse lung tumors |
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