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Series GSE73835 Query DataSets for GSE73835
Status Public on Jun 02, 2017
Title The effect of C/EBPepsilon in differentiated granulocytes: cDNA microarray of C/EBPepsilon knock out mice vs C57BL/6 mice bone marrow cells
Organism Mus musculus
Experiment type Expression profiling by array
Summary To identify target genes of C/EBPepsilon in differentiated granulocytes, total RNA were purified from sorted Gr-1intermediate/Mac-1+ and Gr-1hi/Mac-1+ cells of C/EBPepsilon knock out and C57BL/6 wild type mice using RNeasy Mini Kit (Qiagen). The differences of their expression pattern were compared with Illumina Mouse WG-6v2 Expression Chip platform. Raw Illumina BeadArray data in IDAT format were preprocessed using the open-source Bioconductor package illuminaio with the Illumina array design formation BGX file downloaded from NCBI, GEO accession: GPL6887. Following the preprocessing, the expression data were normalized by applying control background correction, log transformation and inter-quantile normalization using the neqc function from the limma bioconductor package. This allowed us to compare the transcriptomic consequences of C/EBPepsilon in two independent populations.
 
Overall design Sorted Gr-1intermediate/Mac-1+ and Gr-1high/Mac-1+ bone marrow cells from C/EBPepsilon knock out and C57BL/6 wild type mice
 
Contributor(s) Suh HC, Benoukraf T, Yin T, Cao Q, Said J, Lee S, Lim R, Yang H, Shyamsunder P, Madan V, Koeffler HP
Citation(s) 28440307
Submission date Oct 08, 2015
Last update date Jan 16, 2019
Contact name Touati Benoukraf
E-mail tbenoukraf@mun.ca
Phone +1 (709) 864-6671
Organization name Memorial University of Newfoundland
Department Faculty of Medicine, Discipline of Genetics
Street address Craig L. Dobbin Genetics Research Centre,
City St. John's
State/province NL
ZIP/Postal code A1B 3V6
Country Canada
 
Platforms (1)
GPL6887 Illumina MouseWG-6 v2.0 expression beadchip
Samples (6)
GSM1904293 Sorted Gr-1high/Mac-1+ WT
GSM1904294 Sorted Gr-1intermediate/Mac-1+ WT replicate 1
GSM1904295 Sorted Gr-1intermediate/Mac-1+ WT replicate 2
This SubSeries is part of SuperSeries:
GSE73860 Landscape of CEBPe target genes in mouse bone marrow
Relations
BioProject PRJNA298235

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE73835_RAW.tar 28.3 Mb (http)(custom) TAR (of IDAT)
Raw data provided as supplementary file
Processed data included within Sample table

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