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Sample GSM5093689 Query DataSets for GSM5093689
Status Public on Apr 29, 2021
Title clf_Input_rep2_S4
Sample type SRA
 
Source name seedlings
Organism Arabidopsis thaliana
Characteristics genotype: clf mutant
antibody: input
Growth protocol ChIPseq assays were performed on shoot or root of 14‐day‐old seedlings
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were then generated using 10ng of DNA and NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Trimmomatic-0.38: Minimum length of 36 bp; Mean Phred quality > 30; Leading and trailing bases removal with base quality <5. The reads were mapped onto the TAIR10 assembly using Bowtie2 with mismatch permission of 1 bp. MACS2 for peaks detection were set as follows: Number of duplicate reads at a location:1; mfold of 5:50; q-value cutoff: 0.05; extsize 200; broad peak
Genome_build: TAIR10
Supplementary_files_format_and_content: BIGWIG
 
Submission date Feb 19, 2021
Last update date Apr 29, 2021
Contact name Sanchari Sircar
E-mail(s) sancharisircar24@gmail.com
Organization name IPS2
Lab Chromosome Dynamics
Street address Batiment 630 Rue Noetzlin
City Orsay
ZIP/Postal code 75015
Country France
 
Platform ID GPL19580
Series (1)
GSE155502 Polycomb-dependent differential chromatin compartmentalization determines gene co-regulation in Arabidopsis
Relations
BioSample SAMN17998794
SRA SRX10133724

Supplementary file Size Download File type/resource
GSM5093689_ChIP_clf_Input_rep2_s3norm.bw 49.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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