mouse wg-6 v2.0 expression beadchip microarrays  (Illumina Inc)

Journal: Scientific Reports

Article Title: Mapping the chromatin landscape and Blimp1 transcriptional targets that regulate trophoblast differentiation

doi: 10.1038/s41598-017-06859-9

Figure Lengend Snippet: Increased chromatin accessibility leads to activated gene expression during trophoblast differentiation. ( A ) Microarray heatmap of genes differentially expressed during trophoblast differentiation. In contrast to our previous study where we used these data to identify genes differentially expressed between wild type and Prdm1 mutant trophoblasts , here we present gene expression changes during wild type TSC differentiation. ( B ) Heatmap of ATAC-seq read densities at high-confidence TSC and d2 DARs as indicated in B. ( C ) Defined differentially accessible regions (DARs) and corresponding nearest TSSs ±100 kb. ( D ) Distribution of DARs relative to the nearest TSS defined by GREAT . TSC DARs are significantly further from TSSs than d2 DARs – P = 6.0 × 10 −8 , two-tailed homoscedastic t-test. ( E ) Gene Set Enrichment Analysis comparing genes with d2 DARs (nearest TSS ±100 kb) and microarray gene expression changes during TSC differentiation. * P ≤ 1 × 10 −3 . ( F ) TSC and d2 ATAC-seq peaks at the Ovol2 , Tfap2c and Prdm1 loci. RPM = Reads per million. Identified d2 DARs are indicated in grey boxes. Distinct annotated Prdm1 promoters are indicated.

Article Snippet: For gene expression comparison with TSCs published Illumina Mouse WG-6 v2 Expression BeadChips microarray data for ESCs was downloaded from NCBI (GEO accession number GSE46308).

Techniques: Gene Expression, Microarray, Mutagenesis, Two Tailed Test

Journal: Scientific Reports

Article Title: Mapping the chromatin landscape and Blimp1 transcriptional targets that regulate trophoblast differentiation

doi: 10.1038/s41598-017-06859-9

Figure Lengend Snippet: Regulation of trophoblast function and placenta development by genomic loci showing changes in chromatin accessibility during TSC differentiation. ( A ) Functional annotation analysis of genes with d2 DARs (nearest TSS ±100 kb) using GREAT . ( B ) Sequence motifs identified in TSC DARs using MEME-ChIP and associated E value confidence scores. ( C ) Comparison of RLTR13 family repeats located within TSC and d2 DARs, and random genomic regions. ( D ) The percentages of TSC and d2 DARs, and random genomic regions overlapping annotated repeats. Significant under-representation of repeat regions in d2 DARs was determined using Chi-square test. * P = 7.3 × 10 −217 . ( E ) Sequence motifs identified in d2 DARs using MEME-ChIP aligned with published Tfap2c and GATA2 consensus binding motifs , . Both E value confidence scores for de novo motif identification and P value for match to published motif are shown. ( F ) Microarray expression profile of Tfap2c during wild type trophoblast differentiation. ( G ) Overlap of TSC and d2 DARs with published Tfap2c ChIP-seq peaks . See also Supplementary Figure .

Article Snippet: For gene expression comparison with TSCs published Illumina Mouse WG-6 v2 Expression BeadChips microarray data for ESCs was downloaded from NCBI (GEO accession number GSE46308).

Techniques: Functional Assay, Sequencing, Comparison, Binding Assay, Microarray, Expressing, ChIP-sequencing

Journal: Scientific Reports

Article Title: Mapping the chromatin landscape and Blimp1 transcriptional targets that regulate trophoblast differentiation

doi: 10.1038/s41598-017-06859-9

Figure Lengend Snippet: TSC gene expression controlled by the Fgf-dependent transcription factor Esrrb. ( A ) Microarray analysis of Esrrb expression during TSC differentiation. Fold change relative to TSC is shown. Data represents means ±S.E.M., n ≥ 8 per stage. ( B ) Heatmap of TSC and d2 ATAC-seq data at Esrrb TSC ChIP-seq coordinates. ( C ) Overlap of Esrrb ChIP-seq peaks with TSC and d2 DARs. See also Supplementary Figure . ( D ) Gene Set Enrichment Analysis comparing Esrrb ChIP-seq peaks and microarray changes in gene expression at three stages of in vitro differentiation compared with TSCs. * P < 1 × 10 −3 .

Article Snippet: For gene expression comparison with TSCs published Illumina Mouse WG-6 v2 Expression BeadChips microarray data for ESCs was downloaded from NCBI (GEO accession number GSE46308).

Techniques: Gene Expression, Microarray, Expressing, ChIP-sequencing, In Vitro

Journal: Scientific Reports

Article Title: Mapping the chromatin landscape and Blimp1 transcriptional targets that regulate trophoblast differentiation

doi: 10.1038/s41598-017-06859-9

Figure Lengend Snippet: A subset of Blimp1-bound regions may also display Tfap2c occupancy. ( A ) MEME-ChIP analysis of d2 Blimp1 ChIP-seq peaks identified multiple transcription factor binding motifs , , . E value confidence scores for de novo motif identification and P value for match to published motif are shown. ( B ) Overlap of d2 Blimp1 and d1 Tfap2c ChIP-seq peaks. Examples of genes occupied by both Blimp1 and Tfap2c at overlapping coordinates ±100 kb of their TSS are indicated. See also Supplementary Figure . ( C , D ) Comparison of ATAC-seq and ChIP-seq peaks showing Blimp1 and Tfap2c occupancy at Capn5 ( C) and Zwint ( D ), with microarray expression profiles. Fold change relative to TSC is shown. Data represents means ±S.E.M., n ≥ 6 per genotype per stage. RPM = Reads per million. Gene Set Enrichment Analysis comparing overlapping Blimp1/Tfap2c ChIP-seq peaks and microarray changes in gene expression during TSC differentiation. * P < 5 × 10 −2 .

Article Snippet: For gene expression comparison with TSCs published Illumina Mouse WG-6 v2 Expression BeadChips microarray data for ESCs was downloaded from NCBI (GEO accession number GSE46308).

Techniques: ChIP-sequencing, Binding Assay, Comparison, Microarray, Expressing, Gene Expression

Journal: Scientific Reports

Article Title: Mapping the chromatin landscape and Blimp1 transcriptional targets that regulate trophoblast differentiation

doi: 10.1038/s41598-017-06859-9

Figure Lengend Snippet: Blimp1 target genes govern diverse processes including immunity, vascularity, signalling and invasion. ( A ) Functional annotation analysis of genes with Blimp1 ChIP-seq peaks (nearest TSS ±100 kb) that are upregulated in Prdm1 mutant trophoblasts ( P ≤ 0.05, fold change ≥ 1.5) using Enrichr classified according to Mouse Genome Informatics Phenotype, Gene Ontology Molecular Function and NCBI transcription factor loss-of-function terminology. ( B – F ) Comparison of ATAC-seq and Blimp1 ChIP-seq tracks with microarray expression profiles. Data represents means ±S.E.M., n ≥ 6 per genotype per stage. RPM = Reads per million. ( G ) qRT-PCR validation of Blimp1 target gene expression. * P = 2 × 10 −2 ; ** P = 5 × 10 −4 .

Article Snippet: For gene expression comparison with TSCs published Illumina Mouse WG-6 v2 Expression BeadChips microarray data for ESCs was downloaded from NCBI (GEO accession number GSE46308).

Techniques: Functional Assay, ChIP-sequencing, Mutagenesis, Comparison, Microarray, Expressing, Quantitative RT-PCR, Biomarker Discovery, Targeted Gene Expression

Journal: Scientific Reports

Article Title: Mapping the chromatin landscape and Blimp1 transcriptional targets that regulate trophoblast differentiation

doi: 10.1038/s41598-017-06859-9

Figure Lengend Snippet: Blimp1 represses TSC gene expression and prevents aberrant induction of differentiation genes. ( A ) K-means clustering of microarray expression profiles of the 125 identified Blimp1 target genes during TSC differentiation. Blimp1 direct target genes include both TSC-expressed genes (orange) and those activated during differentiation (purple). Percentages of genes within each cluster are indicated. ( B ) Heatmap and density plot of d2 ATAC-seq reads at Blimp1 ChIP-seq peaks distinguish Blimp1 occupancy at accessible or inaccessible target sites. ( C ) Distance of Blimp1 ChIP-seq peaks from the nearest TSS at accessible or inaccessible chromatin regions categorized as in panel B. Blotplot intervals indicate median, 10 th , 25 th , 75 th and 90 th percentiles. Statistical significance was calculated using two-tailed heteroscedastic t-test. * P = 1.1 × 10 −14 . ( D ) Blimp1 ChIP-seq peak intensities at accessible or inaccessible chromatin regions. Statistical significance was calculated using two-tailed heteroscedastic t-test. FPKM = fragments per kilobase per million reads; * P = 2.4 × 10 −6 . ( E ) Occurrence of the Blimp1 consensus binding motif located within Blimp1 ChIP-seq peaks at accessible or inaccessible chromatin regions. Statistical significance was calculated using two-tailed heteroscedastic t-test. * P = 1.0 × 10 −44 . ( F ) Blimp1 occupancy at closed chromatin corresponds to low complexity repeats homologous to the Blimp1 consensus binding motif. RPM = Reads per million. ( G ) Gene Set Enrichment Analysis of wild type and Prdm1 mutant trophoblast gene expression profiles at day 2 of differentiation in comparison with Blimp1 ChIP-seq peaks at accessible and inaccessible chromatin (nearest TSS ±100 kb annotated). * P < 1 × 10 −3 , FWER P = 5 × 10 −3 . ( H ) Overlap of d2 Blimp1 ChIP-seq peaks with TSC and d2 DARs. See also Supplementary Figure . ( I ) Overlap of d2 Blimp1 ChIP-seq peaks with TSC Esrrb ChIP-seq peaks. See also Supplementary Figure . ( J , K ) Blimp1 and Esrrb occupancy at shared ATAC-seq and ChIP-seq peaks in comparison with microarray expression profiles for Ankmy2 ( J ) and Foxp1 ( K ). Data represents means ±S.E.M., n ≥ 6 per genotype per stage. RPM = Reads per million.

Article Snippet: For gene expression comparison with TSCs published Illumina Mouse WG-6 v2 Expression BeadChips microarray data for ESCs was downloaded from NCBI (GEO accession number GSE46308).

Techniques: Gene Expression, Microarray, Expressing, ChIP-sequencing, Two Tailed Test, Binding Assay, Mutagenesis, Comparison