gm12878 chip seq  (Novus Biologicals)

Journal: Bioinformatics

Article Title: Chrom-Sig: de-noising 1D genomic profiles by signal processing methods

doi: 10.1093/bioinformatics/btaf645

Figure Lengend Snippet: Chrom-Sig results on GM12878 CTCF ChIP-seq and CUT&RUN datasets. (a) Browser views of CTCF binding motifs with orientation (blue triangles) and coverage tracks generated by piling up the original (before Chrom-Sig) and Chrom-Sig ‘pass’ or ‘fail’ reads, accompanied by the peaks called by SICER. (b) Venn diagram of the peaks called on the original and Chrom-Sig ‘pass’ reads pile-up reads using false discovery rate (FDR) of 0.1 and 5000 pseudo-reads, with boxplots of maximum peak intensity for each peak. (c) Number of peaks overlapping CTCF motifs, and top MEME result on the original GM12878 CTCF CUT&RUN data before Chrom-Sig. (d) Similar to panel c for Chrom-Sig ‘pass’ results.

Article Snippet: For example, the GM12878 CTCF ChIP-seq data were originally noisy with a large portion of reads in non-binding sites, but Chrom-Sig with FDR of 0.1 retained only the reads with strong binding ( ).

Techniques: ChIP-sequencing, Binding Assay, Generated

Journal: bioRxiv

Article Title: Chrom-Sig: de-noising 1-dimensional genomic profiles by signal processing methods

doi: 10.1101/2025.08.12.670000

Figure Lengend Snippet: Paired End Example for GM12878 Chrom-Sig results for all paired-end datasets from GM12878 cell-line, visualized in the genome browser. CTCF Motif: CTCF binding sites with orientation. Original: Bedgraph file generated directly from input BAM/bed file. SICER peaks: Bed file result of running SICER algorithm on the original bedgraph file. Chrom-Sig FDR 0.1 pass: pass bedgraph generated from original bedgraph by Chrom-Sig (percentage refers to how many reads were retained by Chrom-Sig result from original bedgraph). SICER peaks (below Chrom-Sig FDR 0.1 pass): Bed file from SICER algorithm run on pass-pileup bed generated by Chrom-Sig. ChromHMM: Chromatin states.

Article Snippet: The analysis looks at GM12878 CTCF ChIP-seq ENCFF355CYX (36,269 peaks original, 24,872 peaks after Chrom-Sig) as well as GM12878 CTCF CUT&RUN replicates 4DNFI2G71DR4 (55,251 peaks original, 22,554 peaks after Chrom-Sig) and 4DNFI9U71IB4 (62,176 peaks original, 19,233 peaks after Chrom-Sig).

Techniques: Binding Assay, Generated

Journal: bioRxiv

Article Title: Chrom-Sig: de-noising 1-dimensional genomic profiles by signal processing methods

doi: 10.1101/2025.08.12.670000

Figure Lengend Snippet: Single End Example Chrom-Sig results for all single-end datasets (all single-end data is from GM12878 cell-line), visualized in the genome browser. CTCF Motif: CTCF binding sites with orientation. Original: Bedgraph file generated directly from input BAM/bed file. SICER peaks: Bed file result of running SICER algorithm on the original bedgraph file. Chrom-Sig FDR 0.1 pass: pass bedgraph generated from original bedgraph by Chrom-Sig (percentage refers to how many reads were retained by Chrom-Sig result from original bedgraph). SICER peaks (below Chrom-Sig FDR 0.1 pass): Bed file from SICER algorithm run on pass-pileup bed generated by Chrom-Sig. ChromHMM: Chromatin states.

Article Snippet: The analysis looks at GM12878 CTCF ChIP-seq ENCFF355CYX (36,269 peaks original, 24,872 peaks after Chrom-Sig) as well as GM12878 CTCF CUT&RUN replicates 4DNFI2G71DR4 (55,251 peaks original, 22,554 peaks after Chrom-Sig) and 4DNFI9U71IB4 (62,176 peaks original, 19,233 peaks after Chrom-Sig).

Techniques: Binding Assay, Generated

Journal: bioRxiv

Article Title: Chrom-Sig: de-noising 1-dimensional genomic profiles by signal processing methods

doi: 10.1101/2025.08.12.670000

Figure Lengend Snippet: CTCF Motif Analyses a) Top enriched motifs, E-value, and matching motifs from MEME-Chip for GM12878 CUT&RUN CTCF 4DNFI2G71DR4 before and after Chrom-Sig. b) Comparison of CTCF motif precision between original data and Chrom-Sig with FDR 0.1 and 5000 pseudo-reads for GM12878 ChIP-seq CTCF ENCFF355CYX, GM12878 CUT&RUN CTCF 4DNFI2G71DR4 and 4DNFI9U71IB4.

Article Snippet: The analysis looks at GM12878 CTCF ChIP-seq ENCFF355CYX (36,269 peaks original, 24,872 peaks after Chrom-Sig) as well as GM12878 CTCF CUT&RUN replicates 4DNFI2G71DR4 (55,251 peaks original, 22,554 peaks after Chrom-Sig) and 4DNFI9U71IB4 (62,176 peaks original, 19,233 peaks after Chrom-Sig).

Techniques: Comparison, ChIP-sequencing

Journal: bioRxiv

Article Title: Chrom-Sig: de-noising 1-dimensional genomic profiles by signal processing methods

doi: 10.1101/2025.08.12.670000

Figure Lengend Snippet: ChromHMM State Annotation Distribution Comparison of the distribution of chromHMM states between original data and Chrom-Sig with FDR 0.1 and 5000 pseudo-reads for K562 RNAPII ChIP-seq ENCFF480AJZ and ENCFF785OCU and GM12878 ATAC-seq ENCFF646NWY. The proportion of enhancer and promotor states increases when Chrom-Sig is applied to the data. Between K562 RNAPII ChIP-seq replicates there is an average of 12.3% higher distribution of enhancers and promotors (ENCFF480AJZ: 77% original vs 87.3% Chrom-Sig and ENCFF785OCU: 76.9% original vs 85.5% Chrom-Sig). In ATAC-seq data, the percentage of transcription and heterochromatin states drops from 28.9% to 12.6% after Chrom-Sig.

Article Snippet: The analysis looks at GM12878 CTCF ChIP-seq ENCFF355CYX (36,269 peaks original, 24,872 peaks after Chrom-Sig) as well as GM12878 CTCF CUT&RUN replicates 4DNFI2G71DR4 (55,251 peaks original, 22,554 peaks after Chrom-Sig) and 4DNFI9U71IB4 (62,176 peaks original, 19,233 peaks after Chrom-Sig).

Techniques: Comparison, ChIP-sequencing