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Sample GSM144624 Query DataSets for GSM144624
Status Public on Oct 11, 2007
Title MSC C Affy
Sample type RNA
 
Source name mouse marrow stromal cells, biological replicate C
Organism Mus musculus
Characteristics Strain: C57BL/6, Sex: Female, Age: Adult, Tissue: Bone marrow (cultured cells), Cell type: Marrow Stromal Cells obtained from the Tulane University Center for Gene Therapy
Growth protocol Femurs and tibiae (cleaned of all connective tissue) were centrifuged to obtain the bone marrow. The cell pellet was resuspended in complete isolation medium (CIM) consisting of RPMI-1640 supplemented with FCS, HS and PenStrep followed by filtration through a 70 µm nylon mesh filter. The cells were plated in 40 ml CIM in a 175-cm2 flask for 24 hours to obtain adherent murine stromal cells (P0). Non-adherent cells were removed by washing with PBS and fresh CIM is added. CIM was added every 3-4 days for a total of 4 weeks. Lifted cells (trpysin-EDTA) were replated (P1) in CIM and CIM replaced every 3-4 days for 1-2 weeks. Cells were lifted and expanded (P2) at (50 cells/cm2) in culture expansion medium (CEM) consisting of: IMDM (Gibco, BRL) with 2mM L-glutamine (Gibco), 100 U/ml penicillin, 100µg/ml streptomycin, 0.25 ?g/ml amphotericin B (Gibco), 10creened FBS (Atlanta biologicals, Lawrenville, GA, Lot C0105) and 10 0.000000e+00quine serum (Hyclone, Lot AQH24495) which is replaced every 3-4 days for 1-2 weeks. Cells were lifted and expanded (P3). Passage 3 cells were either frozen or further expanded as above. Passage 5 frozen cells were obtained from the Tulane University Center for Gene Therapy and thawed and cultured using culture expansion medium (CEM) and serum as recommended by the same center. Briefly, cells were cultured at a plating density of 100 cells/cm2 in CEM in a humidified, 2102, 5% CO2, 37oC incubator. As recommended, a first passage was done one day after thawing and subsequently cells were passaged every six days. RNA samples for gene arrays were taken three days after passaging with plates seeded at 300 cells/cm2 during three consecutive passages (10 population doublings).
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 marrow stromal cells, 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: 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 5.222 0.6655
1427768_s_at 1.112 0.9697
1417728_at 270.1 0.001221
1421879_at 43.99 0.02393
1426362_at 135.4 0.001953
1447616_at 3.404 0.4324
1439541_at 32.83 0.001221
1416683_at 1635 0.0002441
1431091_at 15.91 0.03027
1452992_at 81.17 0.0002441
1451481_s_at 9.466 0.3037
1424883_s_at 2581 0.0002441
1451380_at 281.3 0.0002441
1459952_at 22.47 0.0002441
1430816_at 19.92 0.2461
1448366_at 38.52 0.001221
1452145_at 285.5 0.00415
1437327_x_at 637.8 0.0002441
1458049_at 2.07 0.8054
1445925_at 20.92 0.3662

Total number of rows: 45101

Table truncated, full table size 1115 Kbytes.




Supplementary file Size Download File type/resource
GSM144624.CEL.gz 6.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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