NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1301000 Query DataSets for GSM1301000
Status Public on Mar 01, 2014
Title CLM_627
Sample type genomic
 
Source name colorectal liver metastasis
Organism Homo sapiens
Characteristics tissue: liver
cell type: colorectal liver metastasis
Treatment protocol --
Growth protocol --
Extracted molecule genomic DNA
Extraction protocol Each DNA (250ng gDNA) aliquot was 96 well plate. Then, 24 of the samples on a plate were subjected to treatment with Nsp I restriction enzyme. After inactivation of the restriction enzyme, the sticky ends of the digested DNA were ligated to Nsp I adaptor/primers using T4 ligase. Aliquots from each ligated product were added to four separate plates for PCR amplification using a universal primer. The products of all four PCR reactions for each subject were combined and then purified with purification magnetic beads in 1.5ml microtube. The yield of each amplified DNA sample was assessed by UV spectrophotometry on a microplate reader. Any DNA showing lower than expected yield (≥ 3mg/ml) or an unusual size distribution was flagged and not processed further. Subsequently, each DNA was fragmented between 25 to 125 bp using partial DNase I digestion and the size distribution of the fragmented amplicons assessed by agarose gel electrophoresis (4% agarose in Tris-Acetate-EDTA buffer).
Label biotin
Label protocol The end-labeled products were added to a hybridization solution, denatured, and added to a CytoScan™ HD Array (one array per sample).
 
Hybridization protocol Samples passing these QC steps were next end-labeled with a biotinylated nucleoitde using Terminal Deoxynucleotidyl Transferase (TdT). The end-labeled products were added to a hybridization solution, denatured, and added to a CytoScan™ HD Array (one array per sample).
Scan protocol After hybridization was complete, the DNA sample was removed from each microarray and replaced with Array Holding Buffer. Arrays were then washed on the Fluidics Station 450 using AGCC software (Affymetrix GeneChip® Command Console, Version 3.2.2) This protocol includes 6 cycles of 5 mixes/cycle with low stringency Wash Buffer A (6X SSPE, 0.01% Tween-20) at 25℃ followed by 24 cycles of 5 mixes/cycle with high stringency Wash Buffer B (0.6X SSPE, 0.01% Tween-20) at 45℃. Binding of the biotinylated targets was detected by incubating the array for 10 min in a Streptavidin–Phycoerythrin (SAPE) solution at 25℃ followed by a post stain wash comprised of 6 cycles of 5 mixes/cycle with Wash Buffer A at 25℃. A second round of staining was then completed using a 10 min incubation in Anti-Streptavidin Antibody Stain Solution at 25℃ followed by a third stain for 10 min in SAPE solution at 25℃ and a final wash consisting of 10 cycles of 6 mixes/cycle with Wash Buffer A at 30℃, filling of the array with Array Holding Buffer, and a hold at 25℃.
Data processing Data processing of CEL files was done using Nexus Copy Number 6.1 software
Primary data description: 15 files of triplet pairs of normal, primary colorectal carcinoma and matched liver metastases tissues
 
Submission date Jan 03, 2014
Last update date Mar 01, 2014
Contact name SUN YOUNG LEE
E-mail(s) farhanhaqj@gmail.com
Organization name Asan Medical Center
Street address Olympicro
City Seoul
ZIP/Postal code 138-736
Country South Korea
 
Platform ID GPL16131
Series (1)
GSE53799 CytoScanHD array Data for 15 normal, 15 primary colorectal carcinomas and their 15 matched liver metastases

Supplementary file Size Download File type/resource
GSM1301000_CytoScanHD_11-627LT.CEL.gz 28.8 Mb (ftp)(http) CEL
GSM1301000_CytoScanHD_11-627LT.P_.cyhd.cychp.gz 80.0 Mb (ftp)(http) CYCHP
GSM1301000_CytoScanHD_11-627LT.P_.cyhd.cychp.txt.gz 80.6 Mb (ftp)(http) TXT
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap