|
| Status |
Public on Jun 15, 2017 |
| Title |
Direct and tissue-specific assessment of the damaging potential of regulatory SNPs |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
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. Importantly the approach only requires one DNase-seq dataset per cell-type, from any genotype and is resilient across differing experimental procedures and sequence depths. We have made Sasquatch available as a versatile, high-throughput, webtool incorporating pre-processed human data from the Encode project and we demonstrate its effectiveness using validated causal GWAS SNPs and known polymorphic TF binding sites in erythroid tissues.
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| |
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| Overall design |
2 biological replicates using 2 growth protocols and 2 background controls of DNaseq-seq and 1 replicate and 1 background of ATAC-seq.
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| |
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| Contributor(s) |
Suciu MC, Hughes JR, Schwessinger R |
| Citation(s) |
28904015 |
| |
| Submission date |
Sep 02, 2016 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Jim Hughes |
| E-mail(s) |
jim.hughes@imm.ox.ac.uk
|
| Phone |
1865222113
|
| Organization name |
University of Oxford
|
| Department |
MHU
|
| Lab |
Genome Biology Group
|
| Street address |
Weatherall Institute Of Molecular Me
|
| City |
oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
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| Platforms (3) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (6)
|
| GSM2301521 |
Primary erythroid cells, biological replicate 1, growth protocol 1 (human) |
| GSM2301522 |
Primary erythroid cells, biological replicate 2, growth protocol 2 (human) |
| GSM2301523 |
Deproteinized DNA, genome-wide DNaseI digestion background (human) |
| GSM2301524 |
Deproteinized DNA, genome-wide DNaseI digestion background (mouse) |
| GSM2594182 |
Primary erythroid cells, growth protocol 2_ATAC |
| GSM2594186 |
Deproteinized DNA, genome-wide ATAC transposition background |
|
| Relations |
| BioProject |
PRJNA341669 |
| SRA |
SRP084315 |
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