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Sample GSM133633 Query DataSets for GSM133633
Status Public on Mar 26, 2007
Title SR hg133b21
Sample type RNA
 
Source name lymphoma
Organism Homo sapiens
Characteristics age: 11
cell_type: lymphoma
disease_state: lymphoma
sex: male
Biomaterial provider no institution; W.J. Urba, Program Resources, Inc.;
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;
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;
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;
 
Hybridization protocol na
Scan protocol Affymetrix CEL analysis (Percentile); Protocol Type = feature_extraction; Parameter CellMargin = 2; Parameter OutlierHigh = 1.500; Parameter OutlierLow = 1.004; Parameter Percentile = 75; Software: Affymetrix MicroArraySuite, type: feature_extraction_software;
Protocol Type = image_acquisition; Software: Affymetrix MicroArraySuite, type: image_acquisition_software; Hardware: ;
Description Background Avg = 44.72
Background Max = 47.9
Background Min = 42.8
Background Stdev = 0.95
Central- Avg = 4320
Central- Count = 9
Corner+ Avg = 94
Corner+ Count = 32
Corner- Avg = 5675
Corner- Count = 32
Noise Avg = 1.62
Noise Max = 1.9
Noise Min = 1.4
Noise Stdev = 0.10
RawQ = 1.85
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: blood
Data processing ExpressionStat; Protocol Type = bioassay_data_transformation; Parameter Alpha1 = 0.05; Parameter Alpha2 = 0.065; Parameter BG = 4; Parameter Epsilon = 0.5; Parameter Gamma1H = 0.0045; Parameter Gamma1L = 0.0045; Parameter Gamma2H = 0.006; Parameter Gamma2L = 0.006; Parameter HZ = 4; Parameter NF = 1.000000000000; Parameter Perturbation = 1.1; Parameter SF = 1.000000000000; Parameter SmoothFactorBG = 100; Parameter Tau = 0.015; Parameter VZ = 4; Software: Affymetrix GeneChip Operating Software, type: bioassay_data_transformation_software;
 
Submission date Sep 01, 2006
Last update date Mar 26, 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 GPL97
Series (1)
GSE5720 Comparison between cell lines from 9 different cancer tissue (NCI-60) (U133 platform)

Data table header descriptions
ID_REF The name of the probe set.; Type: string_datatype; Scale: unscaled
CHPPairs The number of probe pairs in the probe set.; Type: integer; Scale: linear_scale
CHPPairsUsed The number of probe pairs in the probe set used in the Detection call.; Type: integer; Scale: linear_scale
VALUE A measure of the relative abundance of a transcript.; Type: float; Scale: linear_scale
CHPDetection A measurement indicating if the transcript was detected (Present), not detected (Absent) or marginally detected (Marginal). Can be one of "A", "M", "P" or "No Call".; Type: string_datatype; Scale: unscaled
CHPDetectionPvalue See Detection p-value; Type: float; Scale: linear_scale

Data table
ID_REF CHPPairs CHPPairsUsed VALUE CHPDetection CHPDetectionPvalue
AFFX-BioB-5_at 20 20 433.0 Present 0.00017
AFFX-BioB-M_at 20 20 2140.7 Present 0.00004
AFFX-BioB-3_at 20 20 1933.2 Present 0.00004
AFFX-BioC-5_at 20 20 90.8 Present 0.00006
AFFX-BioC-3_at 20 20 205.0 Present 0.00007
AFFX-BioDn-5_at 20 20 0.8 Absent 0.97810
AFFX-BioDn-3_at 20 20 1960.9 Present 0.00004
AFFX-CreX-5_at 20 20 633.2 Present 0.00005
AFFX-CreX-3_at 20 20 167.7 Present 0.00007
AFFX-DapX-5_at 20 20 55.9 Present 0.00015
AFFX-DapX-M_at 20 20 123.8 Present 0.00159
AFFX-DapX-3_at 20 20 33.8 Present 0.00202
AFFX-LysX-5_at 20 20 1.1 Absent 0.67292
AFFX-LysX-M_at 20 20 7.4 Absent 0.50000
AFFX-LysX-3_at 20 20 0.8 Absent 0.58862
AFFX-PheX-5_at 20 20 0.3 Absent 0.96034
AFFX-PheX-M_at 20 20 0.4 Absent 0.95352
AFFX-PheX-3_at 20 20 6.3 Absent 0.52976
AFFX-ThrX-5_at 20 20 1.1 Absent 0.88389
AFFX-ThrX-M_at 20 20 1.9 Absent 0.60308

Total number of rows: 22645

Table truncated, full table size 802 Kbytes.




Supplementary file Size Download File type/resource
GSM133633.CEL.gz 3.1 Mb (ftp)(http) CEL

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