|
| Status |
Public on Jul 01, 2011 |
| Title |
PBMC_epimutationpatientI1_rep1 |
| Sample type |
genomic |
| |
|
| Source name |
Peripheral blood lymphocytes, cancer-affected carrier
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
phenotype: cancer-affected carrier of constitutional MLH1 epimutation
family member: I1
family relationship: mother
cell type: peripheral blood lymphocytes
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from peripheral blood lymphocytes (PBL) and lymphoblastoid cell lines (LCL) using the phenol-chloroform method.
|
| Label |
biotin
|
| Label protocol |
Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 User Guide (P/N 702504, Rev 3).
|
| |
|
| Hybridization protocol |
Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 User Guide (P/N 702504, Rev 3).
|
| Scan protocol |
Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 User Guide (P/N 702504, Rev 3), GCFS 450, GCS 3000 HR, AGCC v3.0.
|
| Description |
I1 from Lynch syndrome family 16.
|
| Data processing |
APT v.1.12.0 used for preprocessing. Genotypes determined with apt-probeset-genotype (v. 1.264.2.2) using birdseed-v2 and cn-probe-chrXY-ratio for gender estimation. Intensity probe values extracted using apt-probeset-summarize (v. 1.178) with quant-norm.sketch=0, pm-only, med-polish, expr.genotype=true. The target distributions used for quantile normalization were separately generated on 300 WTCCC control samples (150 58BC and 150 NBS). Data was processed with the PennCNV-Affy routines to yield the 'GSE30348_gw6.lrr_baf.txt' file, which is linked to the Series GSE30348 record as a supplementary file. CNV calling with QuantiSNP, PennCNV and COKGEN.
|
| |
|
| Submission date |
Jun 30, 2011 |
| Last update date |
Jul 01, 2011 |
| Contact name |
Megan P Hitchins |
| E-mail(s) |
m.hitchins@unsw.edu.au
|
| Phone |
61293851431
|
| Fax |
61293851430
|
| Organization name |
University of New South Wales
|
| Department |
Lowy Cancer Research Centre
|
| Lab |
Adult Cancer Program
|
| Street address |
Randwick High Street
|
| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE30348 |
Dominant MLH1 epimutation linked to 5'UTR variant c.-27C>A |
|
