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Series GSE110681 Query DataSets for GSE110681
Status Public on Aug 17, 2018
Title Simplified ChIP-exo assays
Organisms Saccharomyces cerevisiae; Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and its ultra-high resolution cousin ChIP-exo are methods that identify where proteins bind along any genome in vivo. ChIP-exo achieves near-base pair resolution by creating exonuclease stop sites just 5’ to where formaldehyde-induced protein-DNA cross-links occur. Whereas construction of ChIP genomic libraries is straightforward and widely adopted for ChIP-seq, ChIP-exo is technically more involved which has resulted in limited adoption. Here we describe multiple ChIP-exo protocols, each with use-specific advantages and limitations. The new versions are greatly simplified through removal of multiple enzymatic steps. This is achieved in part through the use of Tn5 tagmentation and/or single-stranded DNA ligation. The result is greater library yields, lower processing time, and lower cost. A similar streamlined approach was developed for ChIP-seq, called ChIP-seq 1-step, where library construction is achieved in one-step.
 
Overall design 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/
 
Contributor(s) Rossi MJ, Lai WK, Pugh BF
Citation(s) 30030442
Submission date Feb 15, 2018
Last update date Mar 26, 2019
Contact name Matthew John Rossi
E-mail(s) mjrossi2881@gmail.com
Phone 5709946197
Organization name Penn State University
Department Biochemistry & Molecular Biology
Lab Pugh
Street address 453 N Frear Bldg
City University Park
State/province Pennsylvania
ZIP/Postal code 16802
Country USA
 
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19756 Illumina NextSeq 500 (Saccharomyces cerevisiae)
Samples (67)
GSM3011657 CTCF ChIP-exo 1.1 Replicate 1
GSM3011658 CTCF ChIP-exo 1.1 Replicate 2
GSM3011659 CTCF ChIP-exo 1.1 Replicate 3
Relations
BioProject PRJNA434276
SRA SRP132940

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
GSE110681_Abf1_ChIP-exo1.1_peaks.gff.gz 35.8 Kb (ftp)(http) GFF
GSE110681_Abf1_ChIP-exo3.0_Nextera_peaks.gff.gz 97.2 Kb (ftp)(http) GFF
GSE110681_Abf1_ChIP-exo3.0_peaks.gff.gz 46.4 Kb (ftp)(http) GFF
GSE110681_Abf1_ChIP-exo4.0_peaks.gff.gz 43.3 Kb (ftp)(http) GFF
GSE110681_Abf1_ChIP-exo4.1_peaks.gff.gz 66.2 Kb (ftp)(http) GFF
GSE110681_Abf1_ChIP-exo5.0_peaks.gff.gz 52.5 Kb (ftp)(http) GFF
GSE110681_Abf1_ChIP-seq_peaks.gff.gz 5.2 Kb (ftp)(http) GFF
GSE110681_Abf1_ChIPmentation_peaks.gff.gz 107.5 Kb (ftp)(http) GFF
GSE110681_BY4741_ChIP-exo1.1_peaks.gff.gz 124.6 Kb (ftp)(http) GFF
GSE110681_BY4741_ChIP-exo3.0_peaks.gff.gz 2.3 Kb (ftp)(http) GFF
GSE110681_BY4741_ChIP-exo4.0_peaks.gff.gz 7.1 Kb (ftp)(http) GFF
GSE110681_BY4741_ChIP-exo4.1_peaks.gff.gz 10.7 Kb (ftp)(http) GFF
GSE110681_BY4741_ChIP-exo5.0_peaks.gff.gz 3.0 Kb (ftp)(http) GFF
GSE110681_BY4741_ChIP-seq1step_peaks.gff.gz 1.6 Kb (ftp)(http) GFF
GSE110681_BY4741_ChIPmentation_peaks.gff.gz 5.3 Kb (ftp)(http) GFF
GSE110681_CTCF_ChIP-exo1.1_peaks.gff.gz 10.9 Kb (ftp)(http) GFF
GSE110681_CTCF_ChIP-exo5.0_peaks.gff.gz 6.6 Kb (ftp)(http) GFF
GSE110681_CTCF_ChIP-seq1step_peaks.gff.gz 3.4 Kb (ftp)(http) GFF
GSE110681_CTCF_ChIP-seq_peaks.gff.gz 6.3 Kb (ftp)(http) GFF
GSE110681_NoAb_K562_ChIP-exo1.1_peaks.gff.gz 11.1 Kb (ftp)(http) GFF
GSE110681_NoAb_K562_ChIP-exo3.0_peaks.gff.gz 7.4 Kb (ftp)(http) GFF
GSE110681_NoAb_K562_ChIP-exo5.0_peaks.gff.gz 3.2 Kb (ftp)(http) GFF
GSE110681_NoAb_K562_ChIP-seq1step_peaks.gff.gz 3.0 Kb (ftp)(http) GFF
GSE110681_NoAb_K562_ChIP-seq_peaks.gff.gz 7.1 Kb (ftp)(http) GFF
GSE110681_PolII_ChIP-exo2.0_peaks.gff.gz 8.3 Kb (ftp)(http) GFF
GSE110681_Reb1_ChIP-exo1.1_peaks.gff.gz 55.3 Kb (ftp)(http) GFF
GSE110681_Reb1_ChIP-exo3.0_peaks.gff.gz 32.6 Kb (ftp)(http) GFF
GSE110681_Reb1_ChIP-exo4.0_peaks.gff.gz 58.8 Kb (ftp)(http) GFF
GSE110681_Reb1_ChIP-exo4.1_peaks.gff.gz 32.8 Kb (ftp)(http) GFF
GSE110681_Reb1_ChIP-exo5.0_peaks.gff.gz 42.7 Kb (ftp)(http) GFF
GSE110681_Reb1_ChIP-seq1step_peaks.gff.gz 29.6 Kb (ftp)(http) GFF
GSE110681_Reb1_ChIP-seq_peaks.gff.gz 13.3 Kb (ftp)(http) GFF
GSE110681_Reb1_ChIPmentation_peaks.gff.gz 50.9 Kb (ftp)(http) GFF
GSE110681_Ume6_ChIP-exo1.1_peaks.gff.gz 155.2 Kb (ftp)(http) GFF
GSE110681_Ume6_ChIP-exo3.0_peaks.gff.gz 51.2 Kb (ftp)(http) GFF
GSE110681_Ume6_ChIP-exo4.0_peaks.gff.gz 41.9 Kb (ftp)(http) GFF
GSE110681_Ume6_ChIP-exo4.1_peaks.gff.gz 59.9 Kb (ftp)(http) GFF
GSE110681_Ume6_ChIP-exo5.0_peaks.gff.gz 35.8 Kb (ftp)(http) GFF
GSE110681_Ume6_ChIP-seq_peaks.gff.gz 26.0 Kb (ftp)(http) GFF
GSE110681_Ume6_ChIPmentation_peaks.gff.gz 96.3 Kb (ftp)(http) GFF
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Processed data are available on Series record

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