|
| Status |
Public on Jan 19, 2015 |
| Title |
SKBR3_nascentRNA_SNP6 |
| Sample type |
RNA |
| |
|
| Source name |
Human Breast Cancer Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SK-BR-3
cell type: HER2+
gender: Female
|
| 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 |
total RNA |
| Extraction protocol |
Preparation of samples and analysis of nascent RNA were performed as described previously (Gimelbrant et al., 2007). Briefly, we purified nuclei of assessed cell lines (Nuclei Pure Isolation Kit, Sigma) and subsequently purified nuclear RNA (as described above for total RNA). Then, we hybridized cDNA obtained by reverse transcription of nuclear RNA of each sample onto Affymetrix SNP6.0 arrays.
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
As per manufacturer (Affymetrix)
|
| Scan protocol |
As per manufacturer (Affymetrix)
|
| Data processing |
Data was normalized by Genotyping console and raw single SNP intensities were taken as allelic expression of corresponding genes.
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.
|
| |
|
| 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 |
|
