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Sample GSM1395350 Query DataSets for GSM1395350
Status Public on Nov 05, 2014
Title EC-4-SUPERFICIAL
Sample type genomic
 
Source name EC-4-SUPERFICIAL
Organism Homo sapiens
Characteristics antibody: anti-ETV5
antibody source: ETV5 (H-100)X; sc-22807X; lot#B1904; Rabbit polyclonal IgG; Santa Cruz Biotech, CA, USA
cell type: endometrial carcinoma
tumor region: superficial zone
Extracted molecule genomic DNA
Extraction protocol Upon chromatin cross-linking in 1% formaldehyde, tissue from paired samples corresponding to the superficial zone and invasive front from 6 endometrial carcinomas (30mg) was disaggregated in 600μl of ChIP lysis buffer (PIC, 50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS). After sonication (Branson sonifier 150; Biogen), chromatin fragments (200-1000bp) were pre-cleared with 100 μl of Protein G Agarose/Salmon Sperm DNA beads (Millipore, California, USA). Immunocomplexes of chromatin fragments and ETV5 antibodies (10 µg; Santa Cruz Biotechnologies) were recovered with G protein beads and de-cross-linked (5M NaCl at 65 °C overnight). Resulting DNA was purified using the QIAquick PCR purification kit (Qiagen, Hilden, Germany),
Label biotin
Label protocol Samples were labelled using the GeneChip Wtdouble-Stranded DNA Terminal Labeling Kit according to Affymetrix specifications.
 
Hybridization protocol Samples were prepared and hybridized to GeneChip Human Tiling 1.0R Array according to Affymetrix specifications.
Scan protocol The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 TGPLUS according to manufacturer's instruction.
Data processing Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. CEL files were imported Partek Genomic Suite 6.5 software, pre-normalized using the Robust MultichIp algorithm and converted to log2. With the purpose of detecting genes that ETV5 binds differently at the invasive front, the mean signal from each probe corresponding to the superficial zone was substracted to that of the invasion front across all probes. Statistical parameters were set as p<0.005 (paired t test).
 
Submission date May 21, 2014
Last update date Nov 05, 2014
Contact name Miguel Abal
E-mail(s) miguel.abal.posada@sergas.es
Phone 0034981955073
Organization name University Clinical Hospital
Department Medical Oncology
Lab Translational Oncology Laboratory
Street address Trav Choupana s/n
City Santiago de Compostela
State/province A Coruña
ZIP/Postal code 15706
Country Spain
 
Platform ID GPL5082
Series (1)
GSE57870 ETV5 transcription program links BDNF and promotion of EMT at invasive front of endometrial carcinomas.

Supplementary file Size Download File type/resource
GSM1395350_EC_4_S.CEL.gz 18.6 Mb (ftp)(http) CEL
Processed data are available on Series record

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