sample type: atrophied C26-tumor bearing mice strain: CDF1 gender: male
Treatment protocol
The gastrocnemius/plantaris muscles from a total of 7 mice were used, including 4 C26 tumor-bearing mice, and 3 control non tumor-bearing mice. Gastrocnemius and plantaris muscles were harvested from anesthetized non-tumor and tumor-bearing mice, snap-frozen in liquid nitrogen, and stored at -80°C until further processing.
Growth protocol
Eight-week-old, male CDF1 mice purchased from Charles River Laboratories (Wilmington, MA, USA) were used for all experiments. The use of animals was approved by the Boston University Institutional Animal Care and Use Committee. Animals were maintained on a 12:12 L/D cycle, were housed individually, and were given access to food and water ad libitum. After three days of acclimation, animals were randomly assigned to a non-tumor control group or a C26 tumor-bearing group. Control animals received an inoculum of 150 μL 1 x PBS/matrigel (1:1) subcutaneously into the right and left flanks. Tumor-bearing animals received an inoculum of 5.0 x 105 C26 cells suspended in 150 μL PBS/matrigel (1:1) injected subcutaneously into the right and left flanks.
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. The extracted total RNA was further purified using an RNase-Free DNase I kit (Qiagen, Valencia, CA, USA) and an RNeasy Mini kit (Qiagen, Valencia, CA, USA) as previously described {Wu, 2011 #4036}. Extracted RNA was quantitated by UV spectrophotometry and quality checked by a 1% denaturing agarose gel. Samples were also verified by Bioanalyzer 2100 analysis and had a minimal RIN number of 8.0 (Agilent, Palo Alto, CA, USA).
Label
Btiotin
Label protocol
Whole-transcript expression profiling experiments were carried out by the Boston University Microarray Core Facility. The Affy standard WT Sense Target Labeling assay protocol was followed to synthesize biotinylated DNA.
Hybridization protocol
Fragmented, biotinylated DNA samples were hybridized on a mouse Gene 1.0 ST array acorrding to manufacture's recommendation.
Scan protocol
A total of 6 array images were acquired by GeneChip Scanner 3000 TG and quality assessed by Affymetrix Expression Console (Santa Clara, CA).
Description
Whole transcript expression profiling
Data processing
Gene expression signal values were generated by the Expression File Creator module of the GenePattern platform (Broad Institute, Cambridge, MA) and robust multi-array analysis algorithm (RMA) and quantile normalization was used for data preprocessing {Bolstad, 2003 #4365}. probe group file: MoEx-1_0-st-v1.r2.pgf meta-probeset file: Brainarray MoGene 1.0 ST custom CDF file v.13 was used for probe annotation {Allan, 2005 #4379}.
Cancer-induced Muscle Wasting is IKKβ-dependent and NF-kappaB-independent
Data table header descriptions
ID_REF
VALUE
Gene expression signal values were generated by the Expression File Creator module of the GenePattern platform (Broad Institute, Cambridge, MA) and expressed in log2 ratio
