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Status |
Public on Jan 19, 2015 |
Title |
Wi38_cl1_gDNA_SNP6 |
Sample type |
genomic |
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Source name |
Human Fibroblast
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Organism |
Homo sapiens |
Characteristics |
cell line: WI-38 cell type: Normal_Non tumor gender: Female
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Growth protocol |
WI-38, ZR-75-1, SK-BR-3 and MDA-MB-436 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen) containing 10% fetal bovine serum (FBS).
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Phenol/chlorophrom extraction was used for gDNA isolation
|
Label |
Biotin
|
Label protocol |
As per manufacturer (Affymetrix)
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Hybridization protocol |
As per manufacturer (Affymetrix)
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Scan protocol |
As per manufacturer (Affymetrix)
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Data processing |
Genomic profiling was performed at Institut Curie using Affymetrix SNPChip6.0 array; cell files were processed by Genotyping Console 3.0.2 (Affymetrix, reference model file HapMap270, version 29). SNP array data were mined using the previously described and validated GAP method (Popova et al., 2009). Segmental absolute copy numbers and allelic contents (major allele counts) were detected. R scripts and full details of the application are available at www.bioinfo-out.curie.fr/projects/snp_gap. Each SNP was characterized by (i) global expression level score; (ii) allelic expression ratio score; and (iii) genomic status (loss or retention of heterozygosity score), which were summarized into a bi-allelic and mono- allelic expression status. Genome-wide bi-allelic and mono-allelic expression profiles were obtained by cumulating SNP status in a 50 SNPs window and at gene level.
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Submission date |
Nov 04, 2014 |
Last update date |
Jan 19, 2015 |
Contact name |
Ronan Chaligné |
E-mail(s) |
Ronan.Chaligne@curie.fr
|
Organization name |
Institut Curie
|
Lab |
Edith Heard's lab
|
Street address |
26, Rue d'Ulm
|
City |
Paris |
ZIP/Postal code |
75248 |
Country |
France |
|
|
Platform ID |
GPL6801 |
Series (2) |
GSE62907 |
The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer |
GSE62965 |
Identification of SNPs using genomic DNA and allele specific expression using nascent RNA on snp6 array |
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