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Sample GSM1126209 Query DataSets for GSM1126209
Status Public on Jun 24, 2013
Title FG-3019 treated tumor, biological rep5
Sample type RNA
 
Source name PDA tumor, mouse MH9693, FG-3019, day 9
Organism Mus musculus
Characteristics tissue: pancreatic ductal adenocarcinoma
gender: female
strain: 129/SvJae/C57B6
treatment: FG-3019
Treatment protocol All animal procedures were carried out in accordance with institutional and national guidelines. For matching purposes, LSL-KrasG12D/+;LSL-Trp53R172H/+;Pdx1-Cre (KPC) mice (Hingorani et al. 2005 Cancer Cell 7:469-83.) were screened by high-resolution ultrasound using a Visual Sonics Vevo 2100 System with a MS250, 13-24MHz scanhead. Mice with tumor diameters of 6-9mm were randomized and enrolled into one of four treatment groups: IgG, gemcitabine/IgG, FG-3019, or FG-3019/gemcitabine. Gemcitabine (100mg/kg) was administered every 3-4 days by i.p. injection. Polyclonal human IgG or human monoclonal FG-3019 (30mg/kg) was administered by i.p. injection every 3 days. Tumor volumes were measured on days 4 and 7 by reconstructed 3D ultrasound using the Vevo 2100 software package. Mice were euthanized on day 9, 2h after the final gemcitabine dose, and perfused with PBS. Half of the tumor was fixed with 10% neutral buffered formalin, and the other half was divided into 4-6 pieces, some of which were snap frozen in liquid nitrogen and stored at -80°C, while those to be used for RNA extraction were stored for at least 24hrs in RNAlater (Ambion) at 4°C then snap frozen and stored at -80°C.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the Qiagen RNeasy Universal RNA purification kit per the manufacturer's recommended methods. RNA quantity and integrity were determined using a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano assay kit.
Label biotin
Label protocol Biotinylated cRNA were prepared from 250ng total RNA using the Affymetrix GeneChip 3'IVT Express kit (P/N 901229) according the manufacturer's standard protocol.
 
Hybridization protocol Following fragmentation, labeled cRNA were hybridized on Affymetrix mouse genome 430A 2.0 microarrays using the Affymetrix GeneChip Hybridization, Wash, and Stain kit (P/N 901241) and standard protocol. Hybridization was performed for 16hrs at 45°C, 60rpm in an Affymetrix GeneChip Hybridization Oven 640 and staining and washing were performed using an Affymetrix GeneChip Fluidics Station 450 using the manufacturer's recommended fluidics script for 430Av2 genechips (FS450_0002).
Scan protocol GeneChips were scanned using an Affymetrix GeneChip Scanner 7G. Scanning was performed using AGCC software and resulting CEL files were exported to GCOS v1.4.0.036 to generate CEL files compatible with Agilent GeneSpring GX 7.3.1 analysis software.
Description Tumoral gene expression data from FG-3019 treated mouse MH9693, biological replicate 5
Data processing CEL data were preprocessed using the GC content-based Robust Multi-Array (GCRMA) algorithm and imported into GeneSpring GX 7.3.1. Between-group gene expression comparisons were performed on gene data normalized to the median of measurements in the IgG control samples V1-V7 using parametric t-tests without assuming equal variances or correcting for multiple comparisons.
 
Submission date Apr 18, 2013
Last update date Jun 25, 2013
Contact name Mark D. Sternlicht
E-mail(s) msternlicht@fibrogen.com
Phone 1-415-978-1496
Fax 1-415-978-1908
Organization name FibroGen, Inc.
Department Molecular Biology
Street address 409 Illinois Street
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platform ID GPL8321
Series (1)
GSE46203 Transcriptional effects of CTGF inhibition and gemcitabine in the KPC mouse model of pancreatic ductal adenocarcinoma

Data table header descriptions
ID_REF
VALUE GCRMA processed normalized signal

Data table
ID_REF VALUE
1449064_at 0.818042
1425717_at 0.95607215
1425716_s_at 1.0048506
1425720_at 0.99905837
1449102_at 0.8988581
1448011_at 0.93213904
1448012_at 0.9973058
1448016_at 1.2738144
1448017_at 0.97423697
1429090_at 1.217312
1425715_at 0.89317906
1425436_x_at 0.99828863
1425729_at 1.0020145
1425435_at 0.5748402
1449077_at 0.89501697
1427748_at 1.0603324
1425437_a_at 1.0535431
1426989_at 1.028755
1449082_at 0.8336736
1426389_at 0.82322544

Total number of rows: 22690

Table truncated, full table size 481 Kbytes.




Supplementary file Size Download File type/resource
GSM1126209_MH9693_FG3019_5.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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