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Sample GSM1124938 Query DataSets for GSM1124938
Status Public on Dec 02, 2013
Title KI_TEX_2931_133 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 @52070900803933090410408220339046
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 (
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 Scheelev├Ągen 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

Data table header descriptions
VALUE Normalised signal intensity (log10)

Data table
100121619_TGI_at 8.26
100121620_TGI_at 9.21
100121621_TGI_at 6.2
100121622_TGI_at 4.68
100121623_TGI_at 9.78
100121624_TGI_at 10.16
100121625_TGI_at 8.21
100121626_TGI_at 3.73
100121627_TGI_at 5.55
100121628_TGI_at 4.19
100121629_TGI_at 9.56
100121630_TGI_at 5.12
100121631_TGI_at 3.76
100121632_TGI_at 7.52
100121633_TGI_at 4.69
100121634_TGI_at 3.07
100121635_TGI_at 8.43
100121636_TGI_at 4.86
100121637_TGI_at 6.88
100121638_TGI_at 3.99

Total number of rows: 51562

Table truncated, full table size 1107 Kbytes.

Supplementary file Size Download File type/resource
GSM1124938__52070900803933090410408220339046.CEL.gz 5.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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