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Sample GSM1525799 Query DataSets for GSM1525799
Status Public on Mar 29, 2019
Title CNOT6L WT hepatocytes for Input, biological rep2
Sample type RNA
 
Source name Total RNA of primary hepatocytes from CNOT6L WT mice
Organism Mus musculus
Characteristics gender: Male
strain: C57BL/6J
genotype: Wild-type
tissue: Isolated primary hepatocytes
Growth protocol Primary hepatocytes were isolated from 8-week-old wild-type and Cnot6l KO mice.
Extracted molecule total RNA
Extraction protocol RNA were extracted with Trizol Reagent and GlycoBlue Coprecipitant (Invitrogen) and purified with an RNeasy Kit (Qiagen) according to the manufacturer’s instructions. The quality of RNA was determined using the Bioanalyzer nano chip (Agilent Technologies, Inc.).
Label Biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.
 
Hybridization protocol Following fragmentation, 20 ug of cRNA were hybridized for 16hr at 45C on Gene Chip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.
Description Gene expression data from wild-type primary hepatocytes
Data processing For analysis of microarray data, we extracted and normalized data using robust multi-array averaging implemented in the R package “affy” (www.r-project.org). We used updated probe set definitions because these provide improved precision and accuracy (Sandberg and Larsson, 2007). To identify immunoprecipitated mRNAs, we used analysis of partial variance (APV) and applied the random variance model (RVM) as implemented in the anota R package (Larsson et al., 2010, 2011). In anota we applied the following settings (as defined in the anotaPlotSigGenes function) for gene selection: slopeP=0.01; maxSlope=2; minSlope=(-2); selDeltaP=0.5; selDeltaPT=0.5 and maxRvmP=0.01. This identified genes showing enrichment in immunoprecipitated mRNA from WT cells independent of steady-state mRNA level. The resulting genes were further filtered to identify those enriched in immunoprecipitated mRNA from WT cells (i.e. removed those that were depleted).
 
Submission date Oct 15, 2014
Last update date Mar 29, 2019
Contact name Masahiro Morita
Organization name University of Texas Health Science Center at San Antonio
Department Department of Molecular Medicine
Lab Morita lab
Street address 4939 Charles Katz Drive
City San Antonio
State/province Texas
ZIP/Postal code 78229
Country USA
 
Platform ID GPL7546
Series (1)
GSE62365 RIP-CHIP data from CNOT6L WT and KO hepatocytes

Data table header descriptions
ID_REF
VALUE RMA normalized

Data table
ID_REF VALUE
100009600_at 5.520763046
100012_at 2.975418147
100017_at 8.79463588
100019_at 8.129171622
100034251_at 5.012599613
100036521_at 8.562899674
100037258_at 9.132913
100037278_at 5.610502032
100038570_at 4.853805249
100038635_at 3.625325839
100038680_at 3.492852067
100038887_at 12.97276269
100038959_at 6.940327265
100039026_at 9.092522658
100039027_at 3.056905839
100039094_at 4.555390728
100039235_at 4.434768202
100039282_at 2.824674538
100039284_at 4.464349588
100039307_at 6.232171918

Total number of rows: 16539

Table truncated, full table size 343 Kbytes.




Supplementary file Size Download File type/resource
GSM1525799_CNOT6L_WT_Input_02.CEL.gz 3.8 Mb (ftp)(http) CEL
GSM1525799_CNOT6L_WT_Input_02.CHP.gz 246.5 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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