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Sample GSM3667288 Query DataSets for GSM3667288
Status Public on Nov 28, 2019
Title D17
Sample type genomic
 
Source name Liver
Organism Homo sapiens
Characteristics cell type: Large B-cell lymphopma with IRF4 rearrangement
gender: Male
tissue: FFPE
Treatment protocol none
Growth protocol none
Extracted molecule genomic DNA
Extraction protocol DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted after dewaxing and proteinase K digestion applying standard phenol/chloroform purification procedures
Label Biotin
Label protocol Affymetrix OncoScan™ FFPE Assay kit
 
Hybridization protocol Samples were hybridized onto Affymetrix OncoScan FFPE Assay ki arrays and were washed and stained with GeneChip Fluidics Station 450 (Affymetrix)
Scan protocol Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.
Description Hybridized to Affymetrix OncoScan FFPE Assay
Data processing Nexus biodiscovery 9.0 edition Software
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.
 
Submission date Mar 13, 2019
Last update date Nov 29, 2019
Contact name Joan Enric Ramiz-Zaldivar
E-mail(s) ramis@clinic.cat
Phone +34 932275400
Organization name IDIBAPS
Department Molecular Pathology Laboratory
Lab Centre Esther Koplowitz (CEK)
Street address Rosselló, 153
City Barcelona
ZIP/Postal code 08036
Country Spain
 
Platform ID GPL21558
Series (2)
GSE128215 Large B-Cell Lymphomas in Pediatric and Young Adults Display Clinically Relevant Molecular Features Distinguishable from Adult Counterparts [oncoscan]
GSE128294 Large B-Cell Lymphomas in Pediatric and Young Adults Display Clinically Relevant Molecular Features Distinguishable from Adult Counterparts

Supplementary file Size Download File type/resource
GSM3667288_D17.OSCHP.gz 15.5 Mb (ftp)(http) OSCHP
GSM3667288_D17_A_OncoScan_CNV_.CEL.gz 4.6 Mb (ftp)(http) CEL
GSM3667288_D17_C_OncoScan_CNV_.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data provided as supplementary file

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