anti resource source identifier rabbit polyclonal fancd2 novus biologicals nb100-182  (Novus Biologicals)

Journal: Functional & Integrative Genomics

Article Title: FANCD2 genome binding is nonrandom and is enriched at large transcriptionally active neural genes prone to copy number variation

doi: 10.1007/s10142-024-01453-5

Figure Lengend Snippet: FANCD2 binding is non-random and enriched at transcription start sites. ( A ) Heatmaps of FANCD2 ChIP-seq data from U2OS (OK), HCT116 (FE), and FA-D2 + FANCD2 (BL) cells, before and after aphidicolin (APH) treatment. ( B ) Heatmaps from ENCODE ChIP-seq datasets of DNA binding proteins CTCF, POLR2A, and RAD21 and post-translationally modified histones H3K27ac, H3K27me3, and H4K20me1. Heatmaps were generated relative to the transcription start sites (TSS) (5,000 bp upstream and downstream) of UCSC genes and gene predictions from the GRCh37/hg19 genome assembly. ( C ) Read density plots of CTCF, POLR2A, RAD21, H3K27ac, H3K27me3, H4K20me1(left) and OK, FE and BL ChIP-seq data before and after (APH) treatment (right). Plots were generated relative to TSS. An asterisk (*) and hash (#) symbol are used to clearly distinguish the darker blue lines

Article Snippet: Chromatin immunoprecipitation was performed with rabbit polyclonal anti-FANCD2 antibody (NB100-182, Novus Biologicals).

Techniques: Binding Assay, ChIP-sequencing, DNA Binding Assay, Modification, Generated

Journal: Functional & Integrative Genomics

Article Title: FANCD2 genome binding is nonrandom and is enriched at large transcriptionally active neural genes prone to copy number variation

doi: 10.1007/s10142-024-01453-5

Figure Lengend Snippet: FANCD2 binds to large genes under conditions of replication stress. ( A ) Integrated Genomics Viewer (IGV) snapshot at IMMP2L , NRG3 , DOCK1 , and LARGE1 genomic loci depicting shared and unique FANCD2 occupancy in OK, FE, and BL datasets following aphidicolin (APH) treatment. Specific genomic regions are displayed on top of the graphic. ( B ) Comparison of the gene size distribution of all genes in the human genome to the sizes of genes bound by FANCD2 in OK, FE, and BL datasets. ( C ) Venn diagram of unique and shared FANCD2 binding targets from OK, FE, and BL ChIP-seq datasets. ( D ) List of genes bound by FANCD2 in all three ChIP-seq datasets and their corresponding gene sizes

Article Snippet: Chromatin immunoprecipitation was performed with rabbit polyclonal anti-FANCD2 antibody (NB100-182, Novus Biologicals).

Techniques: Comparison, Binding Assay, ChIP-sequencing

Journal: Functional & Integrative Genomics

Article Title: FANCD2 genome binding is nonrandom and is enriched at large transcriptionally active neural genes prone to copy number variation

doi: 10.1007/s10142-024-01453-5

Figure Lengend Snippet: STRINGdb network analysis reveals FANCD2 binding enrichment at neural genes. ( A ) STRINGdb analysis of FANCD2 broad binding regions (BBRs) highlighting genes implicated in nervous system development in the BL ChIP-seq dataset. ( B ) STRINGdb analysis of FANCD2 BBRs highlighting genes associated with the human phenotype (Monarch) mental or behavioral disorder biomarker in the BL ChIP-seq dataset

Article Snippet: Chromatin immunoprecipitation was performed with rabbit polyclonal anti-FANCD2 antibody (NB100-182, Novus Biologicals).

Techniques: Binding Assay, ChIP-sequencing, Biomarker Discovery

Journal: Functional & Integrative Genomics

Article Title: FANCD2 genome binding is nonrandom and is enriched at large transcriptionally active neural genes prone to copy number variation

doi: 10.1007/s10142-024-01453-5

Figure Lengend Snippet: FANCD2 broad binding regions overlap with regions of the genome prone to mitotic DNA synthesis. ( A ) IGV snapshot of FANCD2 occupancy at the IMMP2L , AUTS2 , and WWOX genes in OK, FE, and BL ChIP-seq datasets with the corresponding MiDAS-seq peaks from HeLa, U2OS, and HS68 cells at the same genomic loci from the Macheret et al. dataset (Macheret et al. ). Specific genomic regions are displayed on top of the graphic. ( B ) Bar graph depicting % region overlap between OK, FE, and BL FANCD2 ChIP-seq datasets and U2OS, HeLa, and HS68 MiDAS-seq data. ( C ) Bar graph depicting % base pair overlap between OK, FE, and BL FANCD2 ChIP-seq datasets and U2OS, HeLa, and HS68 MiDAS-seq data

Article Snippet: Chromatin immunoprecipitation was performed with rabbit polyclonal anti-FANCD2 antibody (NB100-182, Novus Biologicals).

Techniques: Binding Assay, DNA Synthesis, ChIP-sequencing

Journal: Functional & Integrative Genomics

Article Title: FANCD2 genome binding is nonrandom and is enriched at large transcriptionally active neural genes prone to copy number variation

doi: 10.1007/s10142-024-01453-5

Figure Lengend Snippet: FANCD2 broad binding regions overlap with regions that are hotspots for copy number variation. ( A ) IGV snapshot of FANCD2 binding at the AUTS2 , NEGR1 , and WWOX genes with copy number variation gain (green) or loss (orange, red) data from the Wilson et al. study (Wilson et al. ) shown above and below the peak regions, respectively. Specific genomic regions are displayed on top of the graphic. ( B ) Bar graphs depicting % region overlap, and % base pair overlap between the OK, FE, and BL FANCD2 ChIP-seq datasets and copy number variation regions from 090 and HF1 cells from the Wilson et al. study (Wilson et al. )

Article Snippet: Chromatin immunoprecipitation was performed with rabbit polyclonal anti-FANCD2 antibody (NB100-182, Novus Biologicals).

Techniques: Binding Assay, ChIP-sequencing

Journal: Functional & Integrative Genomics

Article Title: FANCD2 genome binding is nonrandom and is enriched at large transcriptionally active neural genes prone to copy number variation

doi: 10.1007/s10142-024-01453-5

Figure Lengend Snippet: Loss of FANCD2 impacts gene expression of FANCD2 target genes. ( A ) Morpheus heatmap analysis of RNA-seq data demonstrating differential expression of FANCD2 broad binding region (BBR) genes in FA-D2 ( FANCD2 −/− ) cells relative to FA-D2 + FANCD2 cells. Genes with increased expression in FA-D2 ( FANCD2 −/− ) cells relative to FANCD2-complemented FA-D2 cells are depicted in red and genes with decreased expression are depicted in blue. ( B ) Log2 fold change expression of FANCD2 BBR genes between FA-D2 + FANCD2 and FA-D2 ( FANCD2 −/− ) cells after APH treatment. Genes upregulated in FA-D2 + FANCD2 cells - with an adjusted P value less than 0.05 and a log2 fold change greater than 1 - are shown in red. Genes downregulated in FA-D2 + FANCD2 cells - with an adjusted P value less than 0.05 and a log2 fold change less than − 1 - are shown in green. ( C ) Normalized read counts of FANCD2 BBR genes after APH treatment. FA-D2 + FANCD2 read counts are shown in blue and FA-D2 ( FANCD2 −/− ) are shown in orange. *, P < 0.05; **, P < 0.01; ***, P < 0.001

Article Snippet: Chromatin immunoprecipitation was performed with rabbit polyclonal anti-FANCD2 antibody (NB100-182, Novus Biologicals).

Techniques: Gene Expression, RNA Sequencing, Quantitative Proteomics, Binding Assay, Expressing