Dataset features

Specifications


Application: ChIP-seq analysis, RNA-seq analysis
Number of samples: 32
Release date: Jan 12 2016
Last update date: Oct 26 2018
Access: Public
Diseases: Colonic Neoplasms, Colorectal Neoplasms
Computational protocol: Sole-Search, BWA, PePr, UCSC Genome Browser
Dataset link Effects on the transcriptome upon deletion of distal elements are not correlated with the size of H3K27Ac peaks in human cells

Experimental Protocol


Analysis of RNA-seq data and ChIP-seq between control clones and enhancer deleted clones in HCT116 cell. For Control, gRNA empty vectorplasmid was transfected with Cas9-GFP. For Deletion, gRNAs that have enhancer target sequences were transfected along with Cas9-GFP. Cells with high GFP expression were identified using fluorescence-activated cell sorting. Sorted cells were plated into individual wells of a 24 well plate and then re-plated as single cells in 10cm dishes and subsequently expanded for further analyses. Samples used in this study were clonal populations. Interaction profiling of enhancers of interest with putative target genes using 4C-seq

Repositories


GEO

GSE72631

ArrayExpress

E-GEOD-72631

ENA

SRP063339

BioProject

PRJNA294738

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