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Sample GSM144642 Query DataSets for GSM144642
Status Public on Oct 11, 2007
Title rClone-2 C Affy
Sample type RNA
Source name rat clone 2, biological replicate C
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 C, 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 5.68900012969971 0.870400011539459
1387978_at 238.100006103516 0.00292999995872378
1372453_at 645.299987792969 0.000244099996052682
1369477_at 41.1199989318848 0.171399995684624
1398287_at 48.8600006103516 0.24609999358654
1376711_at 34.4000015258789 0.0676300004124641
1389774_at 36.3699989318848 0.219500005245209
1371524_at 539 0.000244099996052682
1372087_at 274.5 0.00122099998407066
1368548_at 10.4700002670288 0.149700000882149
1388845_at 13.3000001907349 0.665499985218048
1387020_at 178.300003051758 0.000244099996052682
1371158_at 3.75799989700317 0.962400019168854
1389116_at 262.5 0.000732399988919497
1394180_at 13.210000038147 0.303700000047684
1375416_at 99.6500015258789 0.0461400002241135
1388479_at 530.799987792969 0.00122099998407066
1389528_s_at 498.899993896484 0.000244099996052682
1390526_at 371.200012207031 0.000244099996052682
1374779_at 100.099998474121 0.000732399988919497

Total number of rows: 15923

Table truncated, full table size 697 Kbytes.

Supplementary file Size Download File type/resource
GSM144642.CEL.gz 2.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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