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Series GSE86393 Query DataSets for GSE86393
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.
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.
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
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
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)
BioProject PRJNA341669
SRA SRP084315

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE86393_RAW.tar 1.2 Gb (http)(custom) TAR (of BEDGRAPH, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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