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Series GSE249661 Query DataSets for GSE249661
Status Public on Jul 10, 2024
Title guidedNOMe-seq quantifies chromatin states at single allele resolution for hundreds of custom regions in parallel [guidedNOMe-seq]
Organism Mus musculus
Experiment type Other
Methylation profiling by high throughput sequencing
Summary Since the introduction of next generation sequencing technologies, the field of epigenomics has evolved rapidly. However, most commonly used assays are enrichment-based methods and thus only semi-quantitative. Nucleosome occupancy and methylome sequencing (NOMe-seq) allows for quantitative inference of chromatin states with single locus resolution, but this requires high sequencing depth and is therefore prohibitively expensive to routinely apply to organisms with large genomes. To overcome this limitation, we introduce guidedNOMe-seq, where we combine NOMe profiling with large scale sgRNA synthesis and Cas9-mediated region-of-interest (ROI) enrichment. To facilitate quantitative comparisons between multiple samples, we additionally develop an R package to standardize differential analysis of NOMe-seq data. We extensively benchmark guidedNOMe-seq in a proof-of-concept study, dissecting the interplay of ChAHP and CTCF on chromatin. In summary we introduce a cost-effective, scalable, and customizable targeted enrichment extension to the existing NOMe-seq protocol allowing genome-scale quantification of nucleosome occupancy and transcription factor binding at single allele resolution.
 
Overall design Two sets for guidedNOMe-seq datasets were generated. First, at steady state using biological duplicates of wt, Adnp-/- and Ctcf-FKBP12(F36V) mouse ES cells and second during an Adnp depletion and recovery time-course in Adnp-Avi-3xFLAG-FKBP12(F36V)-mNeonGreen mouse ES cells by dTAG13 treatment for 12h followed by a wash-out for 24h.
 
Contributor(s) Schwaiger M, Mohn F, Kaaij L
Citation(s) 39075377
Submission date Dec 08, 2023
Last update date Oct 03, 2024
Contact name Fabio Mohn
E-mail(s) fabio.mohn@fmi.ch
Organization name Friedrich Miescher Institute for Biomedical Research
Lab Buehler Lab
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (40)
GSM7956956 guidedNOMe-seq in wt mES cells, rep1
GSM7956957 guidedNOMe-seq in wt mES cells, rep2
GSM7956958 guidedNOMe-seq in Adnp knock-out mES cells, rep1
Relations
BioProject PRJNA1050144

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Supplementary file Size Download File type/resource
GSE249661_Nome_matrix_Adnp_timecourse.rds.gz 75.5 Mb (ftp)(http) RDS
GSE249661_Nome_matrix_Adnp_timecourse_replicates_merged.rds.gz 69.9 Mb (ftp)(http) RDS
GSE249661_Nome_matrix_WT_AdnpKO_CtcfKD.rds.gz 33.6 Mb (ftp)(http) RDS
GSE249661_Nome_matrix_WT_AdnpKO_CtcfKD_replicatesMerged.rds.gz 32.5 Mb (ftp)(http) RDS
GSE249661_PCR_Nome_matrix_MotifCentered.rds.gz 204.7 Kb (ftp)(http) RDS
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