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Sample GSM1129684 Query DataSets for GSM1129684
Status Public on Jul 26, 2013
Title Capan-1_parental_rep 1
Sample type RNA
 
Source name Parental cell line 1_3
Organism Homo sapiens
Characteristics sample type: Cell line derived from pancreatic ductal adenocarcinoma
cell line: Capan-1
treatment: control
Treatment protocol Transfections were performed following the manufacturer’s protocols of the TriFECTa Dicer- Substrate RNAi kit (IDT, Coralville, IA, USA) and Lipofectamine RNAi Max Reagent (Invitrogen Corporation, Carlsbad, CA, USA). Cells were transfected with a HOXB7-specific siRNA at a final concentration of 10 nM. The mRNA content was measured 48 hours after transfection by RT-qPCR. Each experiment was repeated at least twice.
Growth protocol Human pancreatic cancer cell line MIA PaCa-2 was obtained from American Type Culture Collection (ATCC® Number: CRL-1420™, Manassas, VA, USA). The cells were maintained routinely in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen Corporation, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS, Invitrogen Corporation), 100 U/mL penicillin G (Invitrogen Corporation), and 0.1 mg/mL streptomycin sulfate (Invitrogen Corporation) at 37°C in a humidified, 5% CO2, 95% air atmosphere. Capan-1 cell line established from a hepatic metastasis of a PDAC was also obtained from ATCC (Number: HTB-79™). The cells were grown in IMDM medium (Invitrogen Corporation) supplemented with 20% FBS (Invitrogen Corporation).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with the RNeasy Plus Mini Kit (Qiagen, Duesseldorf, North Rhine-Westphalia, Germany) according to manufacturer's guidelines.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA, USA) according to the manufacturer's instructions, followed by RNAspin column purification (GE Healthcare, Little Chalfont, Buckinghamshire, UK). Dye incorporation and cRNA yield were checked with the Nanovue Spectrophotometer (GE Healthcare).
 
Hybridization protocol 1.65 µg of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 µL of 2x GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Human GE 4x44K v2 Microarray (G2519F) for 17 hours at 65 ° C rotating at 10 rpm. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute at 37°C with GE Wash buffer 2 (Agilent), 10 seconds with acetonitrile, and 30 seconds with drying solution.
Scan protocol Slides were scanned immediately after washing on the High-Resolution Microarray Scanner (Agilent, Santa Clara, CA, USA) using one color scan setting for 1x44k array slides.
Description Gene expression (parental line)
Data processing The images were captured by the reader Agilent Bundle according to the parameters recommended for bioarrays and extracted by Agilent Feature Extraction software version 9.5.3. Among the spots present in each array only those with none flag (i.e. low intensity, saturation, controls, etc.) were selected for analysis.
 
Submission date Apr 25, 2013
Last update date Jul 28, 2013
Contact name Renato David Puga
Organization name Universidade de São Paulo
Department Instituto de Psiquiatria
Lab Laboratório de Genética
Street address Dr Ovidio Pires de Campos,785
City São Paulo
State/province São Paulo
ZIP/Postal code 05403-010
Country Brazil
 
Platform ID GPL10332
Series (1)
GSE46393 HOXB7 mRNA is overexpressed in pancreatic ductal adenocarcinomas and its knockdown induces cell cycle arrest and apoptosis.

Data table header descriptions
ID_REF
VALUE Agilent Feature Extraction software default normalized log2 signal intensity

Data table
ID_REF VALUE
40261 9.844100945
44515 8.348306348
34356 6.139183367
749 9.55688804
3890 9.813318012
4090 9.737369042
5243 9.856521549
7032 9.820318437
22004 9.767868783
26387 9.981260445
36741 9.790661115
37031 9.759528713
39073 9.819017157
2229 7.725008309
3431 7.681589114
19423 7.951320272
23593 7.951120909
26009 7.717666828
32289 7.736704984
36885 7.765644801

Total number of rows: 43118

Table truncated, full table size 743 Kbytes.




Supplementary file Size Download File type/resource
GSM1129684_US45103074_252665215161_S01_GE1-v5_95_Feb07_1_3.txt.gz 8.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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