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Sample GSM134121 Query DataSets for GSM134121
Status Public on Aug 06, 2007
Title MALME-3M hgu95b
Sample type RNA
 
Source name Malignant melanoma
Organism Homo sapiens
Characteristics MDR Function: 22
Prior Treatment: none
p53 Status: wild type
Age: 43
BioSourceType: other[metastasis]
CellLine: MALME-3M
DiseaseState: Malignant melanoma
Individual:
InitialTimePoint: birth
OrganismPart: skin
Sex: male
TargetedCellType: Malignant melanoma
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 NCI60.26_LABEL30EXTRACT29SUB3
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 GPL92
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
41880_at 189.046867288323 A 0.234556513288975
41881_at 170.193781576381 A 0.520619670302202
41882_at 18.6289224950586 A 0.872354690912682
41883_at 38.4976754963659 A 0.781016771277121
41884_at 11.2034130068088 A 0.956032226962858
41885_at 91.2522803637745 A 0.0604193419667967
41886_r_at 496.307934235786 A 0.0813367142140589
41887_at 32.7876192447242 A 0.918663285785941
41888_at 244.140107026914 A 0.175989407541403
41889_at 38.3521487622011 A 0.910594921500297
41890_at 123.993688942283 A 0.39799368200131
41891_at 70.7494059245597 A 0.302547472472011
41892_at 456.123854322064 A 0.0738301727035754
41893_at 24.44464206602 A 0.861234831712328
41894_r_at 7.20642785616125 A 0.67916990865853
41895_at 384.387304049351 A 0.107301013337028
41896_at 10.6228235885008 A 0.910594921500297
41897_at 164.647302852106 A 0.520619670302202
41898_at 205.604093460356 A 0.162935018869806
41899_at 178.268329482144 A 0.162935018869806

Total number of rows: 12620

Table truncated, full table size 579 Kbytes.




Supplementary file Size Download File type/resource
GSM134121.CEL.gz 2.5 Mb (ftp)(http) CEL
GSM134121.EXP.gz 316 b (ftp)(http) EXP
Processed data included within Sample table

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