Dataset features

Specifications


Application: ChIP-exo analysis
Number of samples: 67
Release date: Aug 17 2018
Last update date: Nov 29 2018
Access: Public
Chemicals: Formaldehyde
Dataset link Simplified ChIP-exo assays

Experimental Protocol


Several versions of optimized ChIP-exo and ChIP-seq protocols are described below: ChIP-exo 1.1 libraries were prepared for sequencing using standard Illumina protocols with a minor modification; Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/ ChIP-exo 1.1 Low Chromatin libraries were prepared for sequencing using standard Illumina protocols with a minor modification; Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/, but used 5 times less starting material was used. ChIP-exo 3.0 libraries were prepared for sequencing using standard Illumina protocols, Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/, with modifications to include a Tn5 transposase to add adapters via tagmentation. Following tagmentation, the ChIP-exo 1.1 protocol was followed. ChIP-exo 3.0 Nextera libraries were prepared as ChIP-exo 3.0, but the in-house Tn5 was replaced by the protein that is commercially available from Illumina. ChIP-exo 4.0 libraries were prepared for sequencing using standard Illumina protocols, Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/, with modifications to the method of adapter ligation. ChIP-exo 4.1 libraries were prepared for sequencing using standard Illumina protocols, Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/, with modifications to the method of adapter ligation. that were opposite polarity of those used in ChIP-exo 4.0. ChIP-exo 5.0 libraries were prepared for sequencing using standard Illumina protocols, Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/ with modifications throughout the protocol that reduced the number of steps and incubation times compared to ChIP-exo 1.1. ChIP-exo 5.0 Low Chromatin Low Chromatin libraries prepared for sequencing as for ChIP-exo 5.0, but used 5 times less starting material was used. ChIP-nexus (ChIP-exo 2.0) libraries were prepared for sequencing using standard Illumina protocols. Reference paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390430/ ChIP-seq 1-step (altChIP-seq) libraries were prepared for sequencing using standard Illumina protocols with modifications that removed standard end repair steps and ligated the adapters in a single step. ChIPmentation (altChIP-seq) libraries were prepared for sequencing using standard Illumina protocols; Reference paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4589892/

Repositories


GEO

GSE110681

ENA

SRP132940

BioProject

PRJNA434276

Download


Contact


Matthew Rossi