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Sample GSM134104 Query DataSets for GSM134104
Status Public on Aug 06, 2007
Title MOLT-4 hgu95e
Sample type RNA
 
Source name Lymphoblastic Leukemia
Organism Homo sapiens
Characteristics MDR Function: 10
Prior Treatment: VB/6MP/Prednisone
p53 Status: wild type
Age: 19
BioSourceType: other[Peripheral Blood]
CellLine: MOLT-4
DiseaseState: Acute Lymphoblastic Leukemia
Individual:
InitialTimePoint: birth
OrganismPart: blood
Sex: male
TargetedCellType: Lymphoblastic Leukemia
TimeUnit: years
Growth protocol NCI60Suspended; RNA harvesting protocol for suspended cells: Media used: RPMI 1640 500 ml FBS 25 ml 200 mM Glutamine 5 ml Cells: start from growing cells from Frederick (not frozen). Started before at passage #8-12. Do not use past passage 20. Grow 10 flasks. 1 flask = ~15 x 106 cells yields ~ 100 ugr RNA. Growth schedule prior to harvest Count cells as necessary to follow growth. Grow cells to ~0.52 x 106 cells /ml Pass 1x106 cells into each T162 w 30 ml media. Pass cells to as many flasks as there are cells for. When passing cells, combine into a single pool. Repeat growth cycle until 10 flasks are available. Refeed Refeed cells the day prior to harvest (without passsing). To do so: Spin down cells 1.7k rpm, 10 min., in a 50 ml tube. Draw off media. Resuspend in 30 ml media. Return to flask. Harvest Harvest at 0.52 x 106cells per ml when 10 flasks are available. Spin 4 flasks of cells at 1.7k rpm (~ 500 x g), 10 min (speed setting at 3.5), in a 250 ml centrifuge tube. Draw off media, leaving ~0.5 ml behind. Flick centirifuge tube to break up cells. Lyse cells in 15 ml lysis buffer (w 10 ul fresh BME per ml) per 4 T162âs. Vortex 10 sec. Draw thru a 20 guage needle 12xâs. Freeze at ö800C. Purify using Quigen Midi Kit.Use a maximum of 100 x 106 cells per column. More will not bind to the column. Company Info: Fetal bovine serum Do not heat inactivate. Bio Whittaker Cat# 14-501F Lot #9S083F 301-898-7025 Quiagen Midi Kit Cat # 75144 DTT Fluka or Gallard 1x PBS pH 7.3-7.5 Bio Whittaker cat #17-516F $5.30 per 500 ml bottle (1-11) 250 ml conical centrifuge 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 Quality Biological, Inc. 301-840-9331 L-glutamine 200 mM, 100x Gibco-BRL cat # 25030-081 162 cm2 flask cat # 3150 Costar Tissue Culture Cell Scrapper, 25cm Sarstedt Cat. # 83.1830 Cells are recieved 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 NCI60.22_LABEL26EXTRACT25SUB3
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 GPL95
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
67022_at 66.5443739265211 A 0.824010592458597
67024_at 446.325620879851 P 0.0130917803336117
67026_at 23.5939884953897 A 0.978133624559143
67028_at 315.764220587651 A 0.284747112241882
67030_at 134.770401760117 A 0.561639122147428
67032_at 173.033969192027 A 0.175989407541403
67035_r_at 11.6704315263581 A 0.982999547252388
67038_at 63.8218811124993 A 0.765443486711025
67040_at 197.300393428104 A 0.458815762471625
67042_at 349.965052712968 A 0.39799368200131
67044_r_at 1122.57537768955 P 0.00261701434183192
67046_at 212.685199717522 A 0.234556513288975
67048_at 138.343062679866 A 0.765443486711025
67049_at 354.811877084192 A 0.189687302191895
67050_at 665.978621628864 A 0.234556513288975
67052_at 1562.58116076785 P 0.0393653623784268
67055_at 330.850758099872 A 0.175989407541403
67058_at 400.389758444924 P 0.00868917034585714
67060_at 368.326463761365 A 0.339557899861190
67062_r_at 29.9732926172663 A 0.926169827296425

Total number of rows: 12639

Table truncated, full table size 575 Kbytes.




Supplementary file Size Download File type/resource
GSM134104.CEL.gz 2.5 Mb (ftp)(http) CEL
GSM134104.EXP.gz 316 b (ftp)(http) EXP
Processed data included within Sample table

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