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Sample GSM144631 Query DataSets for GSM144631
Status Public on Oct 11, 2007
Title mClone-3 A Affy
Sample type RNA
 
Source name mouse clone 3, bone marrow 1, biological replicate A
Organism Mus musculus
Characteristics Strain: C57BL/6, Sex: Male, Age: Adult, Tissue: Bone marrow (cultured cells), Cell type: clone isolated using Multipotent Adult Progenitor Cells culture conditions
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 mouse clone 3, bone marrow 1, 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 (1)
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 3.344 0.6338
1427768_s_at 1.541 0.8286
1417728_at 162.6 0.008057
1421879_at 30.23 0.06763
1426362_at 59.54 0.001221
1447616_at 4.024 0.2742
1439541_at 44.77 0.0002441
1416683_at 1194 0.0002441
1431091_at 18.9 0.008057
1452992_at 94.34 0.0002441
1451481_s_at 11.65 0.2195
1424883_s_at 1371 0.0002441
1451380_at 165.9 0.0007324
1459952_at 22.56 0.0007324
1430816_at 45.45 0.01074
1448366_at 27.96 0.02393
1452145_at 1368 0.0002441
1437327_x_at 583.3 0.0002441
1458049_at 4.553 0.7539
1445925_at 10.53 0.6011

Total number of rows: 45101

Table truncated, full table size 1121 Kbytes.




Supplementary file Size Download File type/resource
GSM144631.CEL.gz 6.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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