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Series GSE132906 Query DataSets for GSE132906
Status Public on Sep 28, 2020
Title siQ-ChIP: A reverse-engineered quantitative framework for ChIP-sequencing
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is a key technique for mapping the distribution and relative abundance of histone posttranslational modifications (PTMs) and chromatin-associated factors across genomes. There is a perceived challenge regarding the ability to quantitatively plot ChIP-seq data, and as such, approaches making use of exogenous additives, or “spike-ins” have recently been developed. Relying on the fact that the IP step of ChIP-seq is a competitive binding reaction, we present a quantitative framework for ChIP-seq analysis that circumvents the need to modify standard sample preparation pipelines with spike-in reagents. We also introduce a visualization technique that, when paired with our formal developments, produces a much more rich characterization of sequencing data.
Overall design Examination of H3K27me3 in a wild-type cell line and one treated with the EZH2 inhibitor (EPZ6438).
Examination of H3K9me3 in a wild-type cell line.
Contributor(s) Dickson BM, Tiedemann RL, Chomiak AA, Vaughan RM, Cornett EM, Rothbart SB
Citation(s) 32994221
Submission date Jun 18, 2019
Last update date Dec 07, 2020
Contact name Scott Rothbart
Organization name Van Andel Research Institute
Street address 333 Bostwick Avenue NE
City Grand Rapids
State/province MI
ZIP/Postal code 49503
Country USA
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (9)
GSM3896237 Veh1_H3K27me3
GSM3896238 Veh2_H3K27me3
GSM3896239 EPZ1_H3K27me3
BioProject PRJNA549445
SRA SRP201748

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

Supplementary file Size Download File type/resource
GSE132906_H3K9me3.HCT116.broadPeak.gz 2.1 Mb (ftp)(http) BROADPEAK
GSE132906_RAW.tar 3.0 Gb (http)(custom) TAR (of BED, BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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