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Sample GSM134013 Query DataSets for GSM134013
Status Public on Aug 06, 2007
Title BT-549 hgu95d
Sample type RNA
 
Source name Papillary infiltrating ductal carcinoma
Organism Homo sapiens
Characteristics MDR Function: -45
Prior Treatment: unknown
p53 Status: unknown
Age: 72
BioSourceType: other[metastasis]
CellLine: BT-549
DiseaseState: Invasive Papillary Breast Carcinoma
Individual:
InitialTimePoint: birth
OrganismPart: breast
Sex: female
TargetedCellType: Papillary infiltrating ductal carcinoma
TimeUnit: years
Growth protocol NCI60Adherent; RNA harvesting protocol for adherent cells Media used: RPMI 1640 500 ml FBS 25 ml -use the DTP serum if possible, from Bio Whittaker, not heat inactivated 200 mM Glutamine 5 ml 1 flask = ~15 x 106 cells yields ~ 100 ugr RNA. Grow 10 flasks. Cells: start from growing cells from Frederick (not frozen). Started before at passage #8-12. Do not use past passage 20. Growth schedule prior to harvest: Grow cells to ~80 confluencey. Trypsinize cells with 5 ml try-EDTA per T162, 15 min., 370C. Pipet up and down several times w 10 ml pipet to get good dispersment of cells. Count cells. Pass cells to as many flasks as there are cells for. When passing cells, combine flasks into a single pool. Pass 1x106 cells into each T162 w 30 ml media. Repeat growth cycle until 10 flasks are available. Refeed Refeed cells the day prior to harvest without harvesting). Draw off media (wo cells). Add back media, 30 ml per T162. Add back to T-162âs. 37 deg C, ON Harvest Target confluency 80% # of flasks = 10 Draw off media from 1st flask. Lyse cells in 15 ml lysis buffer (w 10 ul fresh BME per ml). Scrape cells. Draw off media from 2nd flask. Pipet lysis buffer from flask 1 into flask 2. Repeat lysis with up to 4 T162âs. Pipet into 50 ml tube. Repeat w next set of 4 flasks. When done, vortex 10 sec.. Draw lysate thru a 20 guage needle 12xâs. Freeze at ö800C. Purify using Quiagen Midi Kit. Use a maximun of 100 x 106 cells per column. More will not bind to the column. Company Info ------------ Quiagen Midi Kit Cat # 75144 RLT Buffer (lysis buffer) Cat. # 79216 $60-list, $51- discounted 1-800-362-7737 Fetal Bovine Serum 500 ml, list $261- Cat #14-502F Lot # 9S083F Cambrex (old Bio Whittaker) 1-800-638-8174 1x PBS pH 7.3-7.5 Bio Whittaker cat #17-516F $5.30 per 500 ml bottle (1-11) 250 ml conical tubes Corning cat #25350-250 RPMI-1640 wo L-glutamine cat # 12-167F $13.25 per 500 ml bottle (for 1-11 bottles) Cambrex (old Bio Whittaker) Walkersville, Md. 21793 301-898-7025 1-800-638-8174 Trypsin (0.05%)-EDTA (0.1%) In phosphate buffered saline without calcium and magnesium. cat # 118-087-061 $4.20 per 100 ml bottle Quality Biological, Inc. 301-840-9331 L-glutamine 200 mM, 100x Gibco-BRL cat # 25030-149 20 ml 1-800-828-6686 162 cm2 flask cat # 3150 Costar Tissue Culture Cell Scrapper, 25 cm Sarstedt Cat. # 83.1830 Cells are received from Nick Scudiero, E-mail: SCUDIERO@dtpax2.ncifcrf.gov Also trypsin, FBS and glutamine have been coming from there as well.; Protocol Type = grow; Parameter start Time = 0; Parameter min temperature = 37; Parameter media = RPMI 1640,5% FBS, 1% L-Glutamine;
Extracted molecule total RNA
Extraction protocol NCI60 Extraction Protocol; Harvest Target confluency 80% # of flasks = 10 Draw off media from 1st flask. Lyse cells in 15 ml lysis buffer (w 10 ul fresh BME per ml). Scrape cells. Draw off media from 2nd flask. Pipet lysis buffer from flask 1 into flask 2. Repeat lysis with up to 4 T162’s. Pipet into 50 ml tube. Repeat w next set of 4 flasks. When done, vortex 10 sec.. Draw lysate thru a 20 guage needle 12x’s. Freeze at –800C. Purify using Quiagen Midi Kit. Use a maximun of 100 x 106 cells per column. More will not bind to the column. ; Protocol Type = nucleic_acid_extraction; Parameter Extracted product = total RNA; Parameter Amplification = none;
Label biotin
Label protocol Affymetrix Labeling Protocol; The exact protocol is not available. But Standard Operating Proceadure can be found at http://www.affymetrix.com/support/technical/manual/expression_manual.affx or http://www.affymetrix.com/Auth/support/downloads/manuals/expression_ever_manual.zip Manual number: 701025 Revision 6, page 2.1.3; Protocol Type = labeling; Parameter Amount of nucleic acid labeled = 100; Parameter Used Label = biotin; Parameter Amplification = none;
 
Hybridization protocol Affymetrix Hybridization Protocol; The exact protocol is not available. But Standard Operating Proceadure can be found at http://www.affymetrix.com/support/technical/manual/expression_manual.affx or http://www.affymetrix.com/Auth/support/downloads/manuals/expression_ever_manual.zip Manual number: 701025 Revision 6, page 2.2.3; Protocol Type = hybridization; Parameter Chamber type = Affymetrix- GeneChip Hyb Oven 640; Parameter Quantity of label target used = 100; Parameter Time = 100; Parameter Volume = 100; Parameter Temperature = 100;
Scan protocol Affymetrix U95 Scanning Protocol; 100; Protocol Type = image_acquisition; Software: Default scanner software, type: image_acquisition_software; Hardware: Scanning hardware, make: Affymetrix- GeneChip Scanner 3000, type: array_scanner;
Description NCI60.4_LABEL7EXTRACT6SUB3
Data processing MAS5
 
Submission date Sep 01, 2006
Last update date Aug 06, 2007
Contact name Uma T Shankavaram
E-mail(s) uma@mail.nih.gov
Phone 301-496-6718
Organization name NIH
Department NCI
Lab Radiation Oncology Branch
Street address 9000 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL94
Series (1)
GSE5949 Comparison between cell lines from 9 different cancer tissue (NCI-60) (U95 platform)

Data table header descriptions
ID_REF
VALUE
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
67020_at 243.684350120610 A 0.781016771277121
67021_at 206.030365771942 A 0.561639122147428
67023_at 1255.05167059651 A 0.358690519664824
67025_at 93.4299443520012 A 0.982999547252388
67027_at 320.805832770464 A 0.765480631806376
67029_at 360.063163954999 A 0.500000024038353
67031_at 25.1232022798110 A 0.964837186054688
67033_at 707.77872051739 A 0.204022054791118
67034_at 629.547390059013 A 0.234556513288975
67036_at 182.118794922013 A 0.715252887758118
67037_at 498.906613944529 A 0.520619670302202
67039_g_at 58.0776665652876 A 0.732537440226834
67041_at 609.073147239176 A 0.561639122147428
67043_at 247.328603279196 A 0.66044210013881
67045_r_at 25.1344572467061 A 0.99839763870921
67047_at 233.855630234898 A 0.964837186054688
67051_r_at 840.856339873847 P 0.0114473584876184
67053_at 58.6467979412003 A 0.837064981130194
67054_at 536.89874992838 A 0.520619670302202
67056_at 170.380549811915 A 0.837064981130194

Total number of rows: 12644

Table truncated, full table size 572 Kbytes.




Supplementary file Size Download File type/resource
GSM134013.CEL.gz 2.4 Mb (ftp)(http) CEL
GSM134013.EXP.gz 316 b (ftp)(http) EXP
Processed data included within Sample table

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