|
| Status |
Public on Dec 02, 2013 |
| Title |
KI_TEX_1468_36 lymph node |
| Sample type |
RNA |
| |
|
| Source name |
lymph node
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Fine-needle aspirate
tissue: breast cancer regional lymph node metastasis
|
| Growth protocol |
Fine-needle biopsies of metastases were immersed into RNAlater immidiately after collection.
|
| 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 |
@52070900803933090410408220339057
Gene expression data from breast cancer metastasis sampled before commencement of treatment for metatsatic disease
|
| Data processing |
Data were processed using the QC-RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).
|
| |
|
| Submission date |
Apr 17, 2013 |
| Last update date |
Dec 03, 2013 |
| Contact name |
Siker Kimbung |
| Organization name |
Lund University
|
| Department |
Department of Oncology and Pathology, Clinical Sciences, Lund
|
| Lab |
Lund University Cancer Center/Medicon Village/ Building 404:C2
|
| Street address |
Scheelevägen 2
|
| City |
Lund |
| ZIP/Postal code |
SE-22381 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL10379 |
| Series (1) |
| GSE46141 |
Expression data from fine-needle aspiration biopsies of breast cancer metastases from different anatomical sites |
|
