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Sample GSM585579 Query DataSets for GSM585579
Status Public on Jul 02, 2013
Title MEF b1 integrin YYFF_L4 rep 2
Sample type RNA
Source name Mouse embryonic fibroblast
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: b1 integrin YYFF
cell type: Mouse embryonic fibroblast
developmental stage: prepared from E13.14
sex: female
immortalization: SV-40 large T
Treatment protocol The b1YYFF integrin mutation renders MEFs incapable of executing cytokinesis on b1 integrin specific matrixes. Repeated cytokinesis failure was induced by plating the clones on the β1 specific matrix component laminin in serum-free hybridoma medium over night. Normal medium was added the following day to allow for adhesion via β1 and β3 integrins and thus execution of normal cytokinesis. This procedure was repeated 4 or 8 times after which the cells were grown under normal conditions on plastic.
Growth protocol MEFs were grown in high clucose DMEM supplemented with 10% FBS, 1% L-glutamine and 1% Penicillin/Streptomycin
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using QIAGEN RNeasy mini handbook protocol.
Label biotin
Label protocol For the Illumina gene expression analysis, 100 ng of purified total RNA was amplified and biotinylated in an overnight in vitro transcription reaction using the Illumina RNA TotalPrepTM amplification kit (Ambion, Applied Biosystems).
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description 3A3L4_2
Data processing The data were normalized using quantile normalisation with limma in R
Submission date Aug 20, 2010
Last update date Jul 02, 2013
Contact name Gunilla Högnäs
Organization name VTT
Department Medical Biotechnology
Street address Tykistökatu 6 B
City Turku
ZIP/Postal code 20521
Country Finland
Platform ID GPL6885
Series (1)
GSE23729 The effect of aneuploidy on gene expression

Data table header descriptions
VALUE quantile normalized signal intensity
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 1265.057625 0
ILMN_2721178 323.6556688 0
ILMN_3033922 947.296375 0
ILMN_3092673 3211.13375 0
ILMN_2816356 147.8277313 0.003759399
ILMN_2808939 1423.16375 0
ILMN_2634564 837.1776125 0
ILMN_2737647 70.63856375 0.2343358
ILMN_2734484 294.3594938 0
ILMN_2952292 207.4671938 0
ILMN_2699078 62.97097 0.39599
ILMN_1213681 196.3283938 0
ILMN_2735413 72.47238063 0.2130326
ILMN_2735415 80.35871688 0.1491228
ILMN_2891688 551.9219063 0
ILMN_2637698 1626.566313 0
ILMN_2674228 465.1192 0
ILMN_2601546 76.12723688 0.1766917
ILMN_1230831 58.91149938 0.5100251
ILMN_2848071 80.75320875 0.1453634

Total number of rows: 25697

Table truncated, full table size 803 Kbytes.

Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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