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Sample GSM133638 Query DataSets for GSM133638
Status Public on Mar 26, 2007
Title UO-31 hg133a21
Sample type RNA
 
Source name renal cell carcinoma
Organism Homo sapiens
Characteristics age: unknown
cell_type: renal cell carcinoma
disease_state: renal cell carcinoma-very poorly differentiated
sex: male
Biomaterial provider NCI; W.M.Linehan, no pub
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;
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 = 46.48
Background Max = 48.6
Background Min = 44.9
Background Stdev = 0.90
Central- Avg = 807
Central- Count = 9
Corner+ Avg = 46
Corner+ Count = 32
Corner- Avg = 877
Corner- Count = 32
Noise Avg = 2.32
Noise Max = 2.8
Noise Min = 2.0
Noise Stdev = 0.12
RawQ = 2.02
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: kidney
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 Sep 01, 2016
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 GPL96
Series (1)
GSE5720 Comparison between cell lines from 9 different cancer tissue (NCI-60) (U133 platform)
Relations
Reanalyzed by GSE86363

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 20 855.5 Present 0.00006
AFFX-BioB-M_at 20 20 3779.4 Present 0.00004
AFFX-BioB-3_at 20 20 3485.5 Present 0.00004
AFFX-BioC-5_at 20 20 134.9 Present 0.00045
AFFX-BioC-3_at 20 20 281.5 Present 0.00005
AFFX-BioDn-5_at 20 20 1.5 Absent 0.93232
AFFX-BioDn-3_at 20 20 4121.3 Present 0.00004
AFFX-CreX-5_at 20 20 1336.0 Present 0.00005
AFFX-CreX-3_at 20 20 298.6 Present 0.00007
AFFX-DapX-5_at 20 20 89.0 Present 0.00006
AFFX-DapX-M_at 20 20 185.0 Present 0.00125
AFFX-DapX-3_at 20 20 75.0 Present 0.00141
AFFX-LysX-5_at 20 20 4.4 Absent 0.44065
AFFX-LysX-M_at 20 20 1.8 Absent 0.86052
AFFX-LysX-3_at 20 20 11.5 Absent 0.20573
AFFX-PheX-5_at 20 20 1.0 Absent 0.96034
AFFX-PheX-M_at 20 20 1.7 Absent 0.79427
AFFX-PheX-3_at 20 20 6.2 Absent 0.68628
AFFX-ThrX-5_at 20 20 2.6 Absent 0.71226
AFFX-ThrX-M_at 20 20 3.8 Absent 0.72485

Total number of rows: 22283

Table truncated, full table size 814 Kbytes.




Supplementary file Size Download File type/resource
GSM133638.CEL.gz 3.3 Mb (ftp)(http) CEL

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