gm12878 chip seq Search Results


gm12878 ctcf chip seq encff355cyx  (Chrom Tech)
86
Chrom Tech gm12878 ctcf chip seq encff355cyx
Paired End Example for <t>GM12878</t> 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.
Gm12878 Ctcf Chip Seq Encff355cyx, supplied by Chrom Tech, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/gm12878+chip+seq/bio_rxiv__2025__08__12__670000-105-4-14?v=Chrom+Tech
Average 86 stars, based on 1 article reviews
gm12878 ctcf chip seq encff355cyx - by Bioz Stars, 2026-07
86/100 stars
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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.

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

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.

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

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.

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

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.

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