|
| Status |
Public on Nov 03, 2014 |
| Title |
35_52070900803933090410408220339082 |
| Sample type |
RNA |
| |
|
| Source name |
Breast cancer metastasis
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Fine-needle aspirate
anatomical site: Liver
pam50 subtype: LumB
esr1 module tertile: 2
erbb2 module tertile: 1
aurka module tertile: 1
plau module tertile: 0
vegf module tertile: 1
stat1 module tertile: 1
casp3 module tertile: 0
ras module tertile: 1
mapk module tertile: 1
pten module tertile: 1
akt/mtor module tertile: 0
igf1 module tertile: 0
src module tertile: 2
myc module tertile: 1
e2f3 module tertile: 2
betac module tertile: 2
pik3ca module tertile: 0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification. The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cRNA.
|
| |
|
| Hybridization protocol |
GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.
|
| Scan protocol |
Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.
|
| Description |
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metastatic disease
|
| Data processing |
Data were processed in the open source software R using the RMA algorithm as deployed from with the aroma.affymetrix package
|
| |
|
| Submission date |
Apr 03, 2014 |
| Last update date |
Nov 03, 2014 |
| Contact name |
Nicholas Tobin |
| E-mail(s) |
tobin.nick@gmail.com
|
| Phone |
+46 761966368
|
| Organization name |
Karolinska Institutet
|
| Street address |
Cancer Center Karolinska
|
| City |
Stockholm |
| State/province |
N/A |
| ZIP/Postal code |
17176 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL10379 |
| Series (1) |
| GSE56493 |
Expression data from fine-needle aspiration biopsies of breast cancer metastases from different anatomical sites |
|
