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Protocol publication

[…] used for the overlap studies , . All Italian, Singapore-Chinese and 1000 Genome Project's rare and prevalent variants were tested for overlap with the TFBSs and compared to randomly selected UCE positions (G/C content corrected). Random UCE sets contained equal number of positions to the rare or prevalent variants in the corresponding data sets., For the Super-Enhancer SNVs overlap, one hundred sets of 1000 random rare or prevalent SNVs were selected and each set was tested for TFBSs overlap. From this the mean overlap and 95% confidence intervals was calculated. Random positions selection and all overlap studies were done by BEDTools shuffleBed and intersectBed tools, respectively ., 1000 Genome phase1 version3 variants were downloaded from ., Super-enhancer regions were obtained from the study by Whyte . Mouse to human conversion was done by the liftOver tool (, RNA secondary structure predictions were made by RNAsnp perl script which allows large-scale analysis . RNSsnp Mode 1 was used with default parameters, except minimum length of the sequence interval was set to 25. Parameter descriptions can be found from the RNAsnp Web Server (, All statistical calculations and figures were produced using R and its packages., We analyzed single nucleotide variations (SNVs) within 2884 UCE regions that span ∼1.39 Mb of the human genome (). In order to resequence this relatively large set of elements in a comprehensive and economical manner we used a pooled sample targeted sequencing strategy, a cost effective and reliable approach for population resequencing studies , . We had access to samples from two different ancestries: 501 samples from an Italian population (ITA) and 280 samples from a Singaporean Chinese cohort (SG-CHN) (). All samples were pooled by population and gender w […]

Pipeline specifications

Software tools BEDTools, liftoveR, RNAsnp Web Server
Organisms Homo sapiens