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Series GSE172260 Query DataSets for GSE172260
Status Public on Jun 30, 2023
Title Comprehensive characterization of cistrome and epicistrome involved in fruit ripening [red fruit]
Organism Solanum lycopersicum
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The biggest advantage of DAP-seq is that it’s capable of measuring the influence of DNA methylation on TF binding, without disturbing of other epigenetic markers. Here, by utilizing DNA affinity purification sequencing, we generated two binding sets which were incubated with DNA libraries that representing methylomes in different developmental stage. And we made the most of our data to predict DNA methylation impact on TF binding in two dimensions: prediction by comparing genome-wide binding signal in motif-matched regions with or without methylation in single stage, and prediction by comparing binding signal variation in motif-matched regions with or without methylation variation.
 
Overall design DAP-seq of 120 TFs of tomato in red stage.
 
Contributor(s) Lang Z
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Apr 16, 2021
Last update date Jun 30, 2023
Contact name Yu Ma
E-mail(s) may3@sustech.edu.cn
Organization name Southern University of Science and Technology
Street address 1088 Xueyuan Bivd, Nanshan District
City Shenzhen
ZIP/Postal code 518000
Country China
 
Platforms (1)
GPL29032 NextSeq 550 (Solanum lycopersicum)
Samples (393)
GSM5250645 Red-HALO-plateA-rep1
GSM5250646 Red-HALO-plateA-rep2
GSM5250647 Red-HALO-plateA-rep3
This SubSeries is part of SuperSeries:
GSE173213 Comprehensive characterization of cistrome and epicistrome involved in fruit ripening
Relations
BioProject PRJNA722537
SRA SRP315148

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
GSE172260_RAW.tar 24.5 Gb (http)(custom) TAR (of BW)
GSE172260_Red-MBD5-plateA.bed.gz 1.4 Mb (ftp)(http) BED
GSE172260_Red-MBD5-plateB.bed.gz 896.3 Kb (ftp)(http) BED
GSE172260_Red-MBD5-plateCN.bed.gz 1.4 Mb (ftp)(http) BED
GSE172260_Red-MBD5-plateD.bed.gz 1.5 Mb (ftp)(http) BED
GSE172260_Red-MBD5-plateF.bed.gz 1.4 Mb (ftp)(http) BED
GSE172260_Red-MBD5-plateSR.bed.gz 1.9 Mb (ftp)(http) BED
GSE172260_processed_txt_files.tar.gz 20.9 Mb (ftp)(http) TAR
GSE172260_readme.txt 4.3 Kb (ftp)(http) TXT
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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