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Sample GSM144641 Query DataSets for GSM144641
Status Public on Oct 11, 2007
Title rClone-2 B Affy
Sample type RNA
Source name rat clone 2, biological replicate B
Organism Rattus norvegicus
Characteristics Strain: Fisher, Sex: Male, Age: Adult, Tissue: Bone marrow (cultured cells), Cell type: Clone isolated using Multipotent Adult Progenitor Cells culture conditions
Growth protocol Fisher rat BM cells were plated on 600w glucose DMEM, 40% MCDB-201, 1X insulin-transferrin-selenium (ITS; Sigma), 1X LA-BSA, 0.05x10-6M dexamethasone (Sigma), 10-4M ascorbic acid 3-phosphate, 100 units of penicillin, 1,000 units of streptomycin, 55 ?M 2-mercaptoethanol, 2 0.000000BS (HyClone; Lot ANL19977), 10ng/mL hPDGF-BB, 10ng/mL mEGF, and 1000 units/mL mLIF in a humidified, 502 and 6% CO2, 37oC incubator. After 4 weeks, CD45+ cells were depleted using a MACS separation CS column, and cells replated at 10 cells/well. Expansion was done by trypsinizing (0.05% trypsin) the cells and replating them every two days at a density of 200 cells/cm2. Cells at population doubling >100 were used for 3 RNA collections for gene arrays
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNAeasy microkit (Qiagen, Valencia, CA), DNAse treatment was performed on column
Label Biotin
Label protocol 200 ng of total cellular RNA was subjected to double amplification. First round of IVT-based, linear amplification was performed using the RiboAmp OA RNA Amplification Kit (Arcturus, Mountain View, CA) followed by labeling with the Enzo Bioarray HighYield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY) according to manufacturer's instructions
Hybridization protocol Samples were hybridized to Affymetrix Rat Expression Set 230A chips (Affymetrix Inc), washed, and scanned at the University of Minnesota Affymetrix Microarray Core Facility as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Protocol EukGE-WS2v4_450
Scan protocol Array was scanned at the University of Minnesota Affymetrix Microarray Core Facility as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Pixel Size 2.5, Filter 570, Scanner ID 50209060, Number of Scans 1, Scanner Type M10
Description rat clone 2, biological replicate B, Affymetrix
Data processing CEL files were loaded into GeneData Expressionist Refiner (GeneData, San Francisco, CA) to assess overall quality and obtain condensed single intensity values per probeset using the Microarray Analysis Suite Statistical algorithm (MAS 5.0). The mean of mean intensity values for all chips (192) was used to normalize the mean intensity of each chip. Normalization Target: 292, Tau: 0.015, Alpha1: 0.04, Alpha2: 0.06
Submission date Nov 15, 2006
Last update date Oct 11, 2007
Contact name Fernando Ulloa Montoya
Phone +32 (0)16 33 02 92
Fax +32 (0)16 33 02 94
Organization name Katholieke Universiteit Leuven
Department Medicine
Lab Stem Cell Institute
Street address Herestraat 49 bus 804
City Leuven
ZIP/Postal code 3000
Country Belgium
Platform ID GPL341
Series (1)
GSE6933 Unique Molecular Signature of Multipotent Adult Progenitor Cells (Affy)

Data table header descriptions
ID_REF Affymetrix Probe ID
VALUE MAS 5-calculated Signal intensity
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call calculated using MAS 5.0

Data table
1374915_at 2.93700003623962 0.850300014019012
1387978_at 253.800003051758 0.00195299996994436
1372453_at 646.599975585938 0.000244099996052682
1369477_at 24.2700004577637 0.171399995684624
1398287_at 31.8700008392334 0.0676300004124641
1376711_at 27.0300006866455 0.0561500005424023
1389774_at 38.7799987792969 0.149700000882149
1371524_at 510.700012207031 0.000244099996052682
1372087_at 309 0.000244099996052682
1368548_at 0.259600013494492 0.601100027561188
1388845_at 5.03399991989136 0.805400013923645
1387020_at 199.800003051758 0.000244099996052682
1371158_at 5.68200016021729 0.828599989414215
1389116_at 208.300003051758 0.000244099996052682
1394180_at 12.3999996185303 0.334500014781952
1375416_at 113.199996948242 0.0302700009196997
1388479_at 517.099975585938 0.000732399988919497
1389528_s_at 544.599975585938 0.000244099996052682
1390526_at 306.899993896484 0.000732399988919497
1374779_at 122.099998474121 0.000244099996052682

Total number of rows: 15923

Table truncated, full table size 699 Kbytes.

Supplementary file Size Download File type/resource
GSM144641.CEL.gz 2.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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