|
| Status |
Public on May 04, 2015 |
| Title |
MCF10 3 |
| Sample type |
RNA |
| |
|
| Source name |
MCF10 breast cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10
|
| Growth protocol |
Cells were growth in DMEM-Glutamax(10% SFB)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from MCF-7 cells and MCF-10A cells and then purified using (Rneasy kit QIAGEN).
|
| Label |
biotin
|
| Label protocol |
Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labelin
|
| |
|
| Hybridization protocol |
Hybridization cocktails containing fragmented and labeled DNA target were prepared and applied to GeneChip Human Splice Junction arrays. Hybridization performed according to standard Affymetrix protocol.
|
| Scan protocol |
Array scanning was performed according to the manufacturer's instruction (Affymetrix)
|
| Data processing |
CHP files representing RMA expression values were generated as follows:
affymetrix-algorithm-name = rma-exon-all : dabg
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HJAY
program-name = Expression Console
Raw data were processed with the Exon Array Computational Tool (Affymetrix). Data analysis and statistical evaluations were performed by Genosplice. https://www.easana.com. We used the cluster transcripts with high and medium confidence in genes with a not significant fold-change. For each gene, a Student?s t-test that compares mean values between the two experimental conditions was performed. This test provides the fold-change and p-value. All the data processing was perforned by Genosplice (www..easana.con)
probe group file: HJAY_r2.pgf
meta-probeset file: HJAY_r2.full.mps
We used the "ProbeSelect" software (Xing et al., 2006) that selects the probesets (only exon probesets, not junction) that have a highly correlated intensity across all samples. We used these probesets to have a global gene value in each sample. The final results include the p-value and the fold-change for each gene Up or Down regulated in MCF7 compared to MCF10. For the exon level analysis, the intensities, up or down regulation in MCF7 with respect to MCF10, and the fold change value for each of the junctions and exon probes, are given for each cassette exon. High and Medium confidence transcript clusters were selected. The final processed data generated by Genosplice is available in the matrix_processed_data.xls (linked as a supplementary file on the Series record). In http://archimedes.imim.es:9007/biomart/martview/ processed ChIP-Seq samples (GSE56826) and alternative splicing events used in this study are available.
|
| |
|
| Submission date |
Jun 21, 2012 |
| Last update date |
May 04, 2015 |
| Contact name |
Eneritz Agirre |
| Organization name |
Karolinska Institutet
|
| Department |
MBB
|
| Lab |
Castelo-Branco, Molecular Neurobiology
|
| Street address |
Solnavägen 9
|
| City |
Stockholm |
| ZIP/Postal code |
17165 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL15106 |
| Series (2) |
| GSE38864 |
A chromatin code for alternative splicing involving a putative association between CTCF and HP1α proteins |
| GSE60094 |
A chromatin code for alternative splicing involving an association between CTCF and HP1α proteins |
|
