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Items: 10

1.

Direct and tissue-specific assessment of the damaging potential of regulatory SNPs

(Submitter supplied) In the era of GWAS and personalized medicine systematically deciphering the impact of non-coding sequence variation on the regulatory genome is a critical bottleneck. Here we present Sasquatch a novel computational approach to estimate and visualize the effects of noncoding-variants on transcription factor (TF) binding using DNase I footprint data. Developed to provide an unbiased approach to prioritise non-coding variants for functional analysis, Sasquatch performs exhaustive, k-mer based analysis of average footprints to determine any k-mers potential for TF binding and quantifies how this is changed by sequence variants. more...
Organism:
Mus musculus; Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL15520 GPL19057 GPL18573
6 Samples
Download data: BEDGRAPH, WIG
Series
Accession:
GSE86393
ID:
200086393
2.

Illumina NextSeq 500 (Mus musculus)

Platform
Accession:
GPL19057
ID:
100019057
3.

Illumina NextSeq 500 (Homo sapiens)

Platform
Accession:
GPL18573
ID:
100018573
4.

Illumina MiSeq (Homo sapiens)

Platform
Accession:
GPL15520
ID:
100015520
5.

Deproteinized DNA, genome-wide ATAC transposition background

Organism:
Homo sapiens
Source name:
Erythroid cells
Platform:
GPL18573
Series:
GSE86393
Download data: WIG
Sample
Accession:
GSM2594186
ID:
302594186
6.

Primary erythroid cells, growth protocol 2_ATAC

Organism:
Homo sapiens
Source name:
Erythroid cells
Platform:
GPL18573
Series:
GSE86393
Download data: WIG
Sample
Accession:
GSM2594182
ID:
302594182
7.

Deproteinized DNA, genome-wide DNaseI digestion background (human)

Organism:
Homo sapiens
Source name:
Erythroid cells
Platform:
GPL18573
Series:
GSE86393
Download data: WIG
Sample
Accession:
GSM2301523
ID:
302301523
8.

Primary erythroid cells, biological replicate 2, growth protocol 2 (human)

Organism:
Homo sapiens
Source name:
Erythroid cells
Platform:
GPL18573
Series:
GSE86393
Download data: BEDGRAPH
Sample
Accession:
GSM2301522
ID:
302301522
9.

Deproteinized DNA, genome-wide DNaseI digestion background (mouse)

Organism:
Mus musculus
Source name:
Erythroid cells
Platform:
GPL19057
Series:
GSE86393
Download data: WIG
Sample
Accession:
GSM2301524
ID:
302301524
10.

Primary erythroid cells, biological replicate 1, growth protocol 1 (human)

Organism:
Homo sapiens
Source name:
Erythroid cells
Platform:
GPL15520
Series:
GSE86393
Download data: WIG
Sample
Accession:
GSM2301521
ID:
302301521
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Supplemental Content

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