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Sample GSM857414 Query DataSets for GSM857414
Status Public on Mar 26, 2012
Title MM_ND2_rep3_batch2
Sample type RNA
 
Source name MEF transduced with NeuroD2 lentivirus
Organism Mus musculus
Characteristics cell type: Neuronally differentiated MEF cells
Treatment protocol P19 cells and MEFs were infected with lentivirus in media containing polybrene (final concentration 8 µg /ml), and after 24 hours the cells were switched into fresh media. MEFs transduced with MyoD were switched to differentiation media (1% heat inactivated horse serum, 10 μg/mL insulin, 10 μg/mL transferrin) 48 hours after infection.
Growth protocol P19 cells were maintained in MEMα as previously described (Farah et al., 2000, PUBMED ID 10648228), and MEFs derived from Myod-/-/Myf5-/- mice were maintained in DMEM with 10% FBS.
Extracted molecule total RNA
Extraction protocol Neuronally differentiated P19 cells were harvested 72 hours after infection. MEFs were harvested 36-40 hours after switching to differentiation media.
Label biotin
Label protocol Biotinylated cRNA were prepared with the Affymetrix One-Cycle Eukaryotic Target Labeling Assay.
 
Hybridization protocol Standard Affymetrix hybridization protocol
Scan protocol Standard Affymetrix scanning protocol
Description 2.MM.ND.3
Data processing Probe intensities were corrected, normalized, and summarized by the simpleaffy package of Bioconductor (Wilson and Miller,2005). Differentially expressed genes were identified by the LIMMA package of Bioconductor (Wettenhall and Smyth, 2004).
 
Submission date Jan 06, 2012
Last update date Apr 05, 2017
Contact name Stephen Tapscott
E-mail(s) stapscot@fredhutch.org
Organization name Fred Hutch Cancer Research Center
Department Human Biology
Lab Tapscott
Street address 1100 Fairview N. Ave
City Seattle
State/province WASHINGTON
ZIP/Postal code 98103
Country USA
 
Platform ID GPL1261
Series (2)
GSE34907 Genetic and epigenetic determinants of neurogenesis and myogenesis [expression profiling]
GSE34908 Genetic and epigenetic determinants of neurogenesis and myogenesis

Data table header descriptions
ID_REF
VALUE RMA normalized

Data table
ID_REF VALUE
1415670_at 10.79395903
1415671_at 11.83218249
1415672_at 11.76739352
1415673_at 9.647294143
1415674_a_at 10.25490505
1415675_at 9.86839087
1415676_a_at 11.56063148
1415677_at 9.926493629
1415678_at 11.38004648
1415679_at 11.54048104
1415680_at 9.721598032
1415681_at 10.05429614
1415682_at 8.791826623
1415683_at 11.23538928
1415684_at 9.203263176
1415685_at 9.28714862
1415686_at 9.769518486
1415687_a_at 13.65396462
1415688_at 10.87884118
1415689_s_at 9.450143427

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM857414_MG430_2.0_06_MM_N-3.CEL.gz 6.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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