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Sample GSM144628 Query DataSets for GSM144628
Status Public on Feb 05, 2007
Title mMAPC-2 A Affy
Sample type RNA
 
Source name mMAPC clone 2, bone marrow 2, biological replicate A
Organism Mus musculus
Characteristics Strain: C57BL/6, Sex: Female, Age: Adult, Tissue: Bone marrow (cultured cells), Cell type: Multipotent Adult Progenitor Cells
Growth protocol BM was plated in 600w glucose DMEM, 40% MCDB-201 containing 10ng/mL mEGF, hPDGF-BB and 1000 units/ml mouse leukemia inhibitory factor (LIF), 2creened fetal calf serum (FCS), 1x selenium-insulin-transferrin-ethanolamine (SITE), 0.2 mg/mL linoleic acid-bovine serum albumin (LA-BSA), 0.8 mg/mL bovine serum albumin, 1x chemically defined lipid concentrate and 1x 2-mercaptoethanol, 100 units of penicillin, 1,000 units of streptomycin in a humidified, 502 and 6% CO2, 37oC incubator. After 4 weeks, CD45+ and Ter119+ 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 100-200 cells/cm2. Cells at population doubling >80 were used 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 100 ng of total cellular RNA was double amplified and labeled with the Two-Cycle Target Labeling and Control Reagents kit P/N 900494 (Affymetrix Inc., Santa Clara, CA) following the manufacturers' protocol.
 
Hybridization protocol Sample was hybridized to Affymetrix mouse 430 2.0 chips, washed, and scanned at the University of Minnesota Affymetrix Microarray Core Facility as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Protocol EukGE-WS2v5_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 1.56. Filter 570. Scanner ID 50209060. Number of Scans 1. Scanner Type M10
Description mMAPC clone 2, bone marrow 2, biological replicate A, 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: 192, Tau: 0.015, Alpha1: 0.05, Alpha2: 0.065
 
Submission date Nov 15, 2006
Last update date Aug 28, 2018
Contact name Fernando Ulloa Montoya
E-mail(s) fernando.ulloamontoya@med.kuleuven.be
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 GPL1261
Series (2)
GSE6291 Transcriptome Analysis Multipotent Adult Progenitor Cells (Affy)
GSE6933 Unique Molecular Signature of Multipotent Adult Progenitor Cells (Affy)
Relations
Reanalyzed by GSE119085

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
ID_REF VALUE DETECTION P-VALUE
1425763_x_at 13.09 0.6011
1427768_s_at 176.2 0.0002441
1417728_at 394.1 0.0007324
1421879_at 27.64 0.2742
1426362_at 455.9 0.0002441
1447616_at 4.814 0.2195
1439541_at 21.91 0.1116
1416683_at 1048 0.0002441
1431091_at 17.99 0.1116
1452992_at 80.39 0.0002441
1451481_s_at 25.89 0.04614
1424883_s_at 3418 0.0002441
1451380_at 94.21 0.01416
1459952_at 51.65 0.0002441
1430816_at 45.75 0.06763
1448366_at 69.55 0.001221
1452145_at 186.1 0.03027
1437327_x_at 1526 0.0002441
1458049_at 5.652 0.8286
1445925_at 38.9 0.3345

Total number of rows: 45101

Table truncated, full table size 1107 Kbytes.




Supplementary file Size Download File type/resource
GSM144628.CEL.gz 6.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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