genechip mouse genome 430 2.0 array oligonucleotide microarray  (Thermo Fisher)

Journal: Epigenetics & Chromatin

Article Title: The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner

doi: 10.1186/1756-8935-5-8

Figure Lengend Snippet: Regulation of testis-specific genes by CTCFL. A Heatmap representation of microarray data. We compared five samples from heterozygous and three samples from homozygous Ctcfl knockout mice. Depicted are the top 27 deregulated genes, where the log2-transformed fold change compared to the average expression in heterozygous testis is shown. B Expression analyses in Ctcfl mutant testes. Real-time RTPCR expression analyses on testis RNA from Ctcfl mutant mice relative to wild type using Ccna1 as reference. Genes were examined in 90-day-old testes. C Reduced PRSS50 expression in Ctcfl mutant testis. Immunofluorescence analysis of testis sections from heterozygous (del/+) and homozygous (del/del) Ctcfl knockout mice, using antibodies against PRSS50.

Article Snippet: Labeled cRNA was hybridized to the GeneChip Mouse Genome 430 2.0 array oligonucleotide microarray (Affymetrix) according to manufacturer’s recommendations; 300 ng ES cell RNA was used for production of end-labeled biotinylated ssDNA.

Techniques: Microarray, Knock-Out, Transformation Assay, Expressing, Mutagenesis, Reverse Transcription Polymerase Chain Reaction, Immunofluorescence

Journal: Epigenetics & Chromatin

Article Title: The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner

doi: 10.1186/1756-8935-5-8

Figure Lengend Snippet: Genome-wide analysis of CTCFL expression in ES cells. A Inducible expression of CTCFL-V5-GFP in ES cells. Notice the nuclear localization of CTCFL-V5-GFP in cells expressing the protein. B Flow chart of experiments. ES cells with a Tet-on inducible expression of a CTCFLV5-GFP transgene were sorted for GFP and used for microarray and ChIP-Seq analyses. C CTCFL expression and DNA binding are associated with elevated gene expression levels. We plotted gene expression levels, as determined by microarray analysis of induced ( ind ) or non-induced ES cells, for all genes ( all ), or those bound by CTCF, or CTCFL, to the respective promoter region (−2 k to +1 kb around TSS). Differences are highly significant ( p -value CTCF-ind versus CTCFL-ind: 5.1 × e -14 ; p -value CTCF versus CTCFL: 5.9 × e -13 ). D Transcript analyses in ES cells expressing CTCFL-V5-GFP. Real-time RT-PCR expression analyses of CTCFL-V5-GFP-induced and GFP-sorted ES cells, relative to non-induced ES cells, for the indicated genes, referenced to Cdk2 expression. E Venn diagram of DNA-binding sites for CTCFL and CTCF. F Clustered heatmap representation of three classes of CTCF/CTCFL-binding sites. Shown are the binding profiles of CTCFL and CTCF ( 1 : our own data; 2 : ) across all CTCF/CTCFL-binding sites identified in mES cells. Sites are grouped into CTCFL-only, CTCF-only, and combined CTCFL and CTCF sites. Within the three classes, data sets were sorted decreasingly from top to bottom for average binding across the interval from 2 kb to +2 kb around the identified binding peak center positions. Additionally the occurrences of predicted CTCFL motifs within these intervals are plotted. G Motif comparison of CTCF and CTCFL. DNA-binding motif for CTCFL-only ( top panel ), CTCF + CTCFL ( middle panel ) and CTCF-only binding sites ( bottom panel ).

Article Snippet: Labeled cRNA was hybridized to the GeneChip Mouse Genome 430 2.0 array oligonucleotide microarray (Affymetrix) according to manufacturer’s recommendations; 300 ng ES cell RNA was used for production of end-labeled biotinylated ssDNA.

Techniques: Genome Wide, Expressing, Microarray, ChIP-sequencing, Binding Assay, Quantitative RT-PCR