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Sample GSM1181340 Query DataSets for GSM1181340
Status Public on Oct 31, 2013
Title BR:BT_549_rep1
Sample type genomic
 
Channel 1
Source name Papillary infiltrating ductal carcinoma-mammary gland; breast
Organism Homo sapiens
Characteristics cell line: BR:BT_549
Treatment protocol Untreated
Growth protocol Cells grown in RPMI 1640 with 5% FBS (Bio Whittaker, not heat inactivated) and 1% L-glutamine. Cells not grown past 80% confluencey for attached cells, or 0.5 x 10^6 cells for suspended. Trypsinize (for attached cells) cells with 5 ml trypsin-EDTA per T162, for 15 min., at 37C. Spin down suspended cells, and resuspend in ~3ml growth media. Count cells. Pass 1x10^6 cells into new T162's w 30 ml media. Repeat growth cycle until desired amount of cells are available. Cells are not grown past passage 20.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was purified from cells using either the QIAamp DNA Blood Maxi Kit, or the Blood & Cell Culture DNA Maxi Kit (Qiagen Inc., Valencia, CA) according to manufacturer's instructions. Quality was assessed by optical density 260/280 ratio using a spectrophotometer (Beckman-Coulter, Fullerton, CA) and by 0.8% agarose (SeaKem GTG, FMC BioProducts, Rockland, ME) gel electrophoresis in 1x TAE (Roche, Indianapolis, IN).
Label Cy5
Label protocol Done according to array manufacturer's specifications.
 
Channel 2
Source name Reference
Organism Homo sapiens
Characteristics cell line: Reference
Treatment protocol Untreated
Growth protocol Cells grown in RPMI 1640 with 5% FBS (Bio Whittaker, not heat inactivated) and 1% L-glutamine. Cells not grown past 80% confluencey for attached cells, or 0.5 x 10^6 cells for suspended. Trypsinize (for attached cells) cells with 5 ml trypsin-EDTA per T162, for 15 min., at 37C. Spin down suspended cells, and resuspend in ~3ml growth media. Count cells. Pass 1x10^6 cells into new T162's w 30 ml media. Repeat growth cycle until desired amount of cells are available. Cells are not grown past passage 20.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was purified from cells using either the QIAamp DNA Blood Maxi Kit, or the Blood & Cell Culture DNA Maxi Kit (Qiagen Inc., Valencia, CA) according to manufacturer's instructions. Quality was assessed by optical density 260/280 ratio using a spectrophotometer (Beckman-Coulter, Fullerton, CA) and by 0.8% agarose (SeaKem GTG, FMC BioProducts, Rockland, ME) gel electrophoresis in 1x TAE (Roche, Indianapolis, IN).
Label Cy3
Label protocol Done according to array manufacturer's specifications.
 
 
Hybridization protocol Done according to array manufacturer's specifications
Scan protocol Done according to array manufacturer's specifications
Description BR:BT_549 on Cy5 and Reference on Cy3
Data processing Normalized data consists of log2 transformed sample/reference intensities. Raw data are the scan files from the Agilent scanner.
Log2 ratio of red/green (for arrays where sample=Cy5 and reference=Cy3) or green/red (where sample=Cy3 and reference=Cy5).
 
Submission date Jul 06, 2013
Last update date Oct 31, 2013
Contact name Sudhir Varma
E-mail(s) sudhirv4rma@gmail.com
Organization name HiThru Analytics
Street address 1215 Wessex Pl
City Princeton
State/province NJ
ZIP/Postal code 08540
Country USA
 
Platform ID GPL11068
Series (1)
GSE48568 Agilent-013282 array CGH on NCI-60 cancer cell lines

Data table header descriptions
ID_REF
VALUE Normalized, log2 sample/reference ratio

Data table
ID_REF VALUE
A_14_P112718 0.205423683
A_14_P201353 0.439650054
A_14_P108353 0.865601701
A_14_P129881 0.651425661
A_14_P114030 0.295316365
A_14_P139527 0.371968777
A_14_P118340 0.41943999
A_14_P106890 0.132146782
A_14_P122641 0.395928676
A_14_P107170 0.71980977
A_14_P100766 0.068947354
A_14_P118104 1.061816008
A_14_P117253 0.369851836
A_14_P129407 0.713067326
A_14_P200001 0.370462203
A_14_P103811 0.254754928
A_14_P119666 -0.003328018
A_14_P100799 0.571710094
A_14_P121179 0.432708526
A_14_P115318 0.334419039

Total number of rows: 42725

Table truncated, full table size 1049 Kbytes.




Supplementary file Size Download File type/resource
GSM1181340_US14702384_251328213655_S01_44k_CGH_0605.txt.gz 11.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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