|
| Status |
Public on Oct 09, 2007 |
| Title |
HCC1806 |
| Sample type |
RNA |
| |
|
| Source name |
University of Cambridge
|
| Organism |
Homo sapiens |
| Characteristics |
Plate = 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard Trizol extraction protocol, modified by washing the final RNA pellet with 80% EtOH
|
| Label |
Biotin
|
| Label protocol |
Indirect PCR-based labelling method: Linkers were ligated to the 3' and 5' end of miRNAs, cDNA was synthesized using superscript Reverse Transcriptase, cDNA was labelled (Biotin) and amplified by PCR
|
| |
|
| Hybridization protocol |
15ul sample and 33ul of the bead pool were incubated overnight at 50ºC and washed after 16 hours
|
| Scan protocol |
Median fluorescence intensity values were measured on a Luminex 100 machine
|
| Description |
Breast cancer cell line
|
| Data processing |
Raw values smaller than 1 were set equal to 1. After log2 transformation probes were filtered by requiring each probe to exceed 6 in at least one sample. Systematic probe effects between plates were removed by subtracting differences between the probe median for the samples on a given plate and the probe median for all samples on both plates. Unused probes were removed and replicate probes were summarized by their mean expression profile. Two alternative between-sample normalizations were used: 1) Median centering (VALUE) The sample median was subtracted for each sample. Replicate samples were summarized by their mean expression profile. 2) Control-based normalization (CTRL_BASED_NORM) Control probes used for normalization as indicated in 'USAGE' were median centred. Sample effects were estimated by taking the mean over eight control measurements per sample. Normalization was performed by subtracting the estimated effect for each sample. Replicate samples were summarized by their mean expression profile.
|
| |
|
| Submission date |
Aug 22, 2007 |
| Last update date |
Feb 15, 2024 |
| Contact name |
Leonard Goldstein |
| Organization name |
Garvan Institute of Medical Research
|
| Street address |
384 Victoria St
|
| City |
Darlinghurst |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL5173 |
| Series (1) |
| GSE7842 |
MicroRNA expression profiling of human breast cancer identifies new markers of tumour subtype |
|
