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Sample GSM4705369 Query DataSets for GSM4705369
Status Public on Apr 29, 2021
Title HiChIP-K27-Shoot-rep2
Sample type SRA
Source name HiChIP K27 Shoot rep2
Organism Arabidopsis thaliana
Characteristics genotype: Col0
Growth protocol Hi-ChIP experiments were performed on shoots and roots of 14 day-old-seedlings
Extracted molecule genomic DNA
Extraction protocol Hi-ChIP experiments were performed using the same procedure as in Concia et al., 2020 with either anti-H3K9ac (Millipore 07–352) or anti-H3K27me3 (Millipore 07–449).
Libraries were performed using Tn5 transposase using the same procedure as in Concia et al., 2020.
Hi-ChIP libraries
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Data processing Trimmomatic-0.38 to remove Illumina sequencing adapters. The 5′ and 3′ ends with a quality score below 5 (Phred+33) were trimmed and reads shorter than 30 bp after trimming were dropped. The trimmed files were then processed with HiC-Pro v2.11.1 (Servant et al., 2015). The reads were aligned using Bowtie2 onto the TAIR10 assembly with default settings, except for the parameter “--score-min L, -0.6, -0.8”.
Genome_build: TAIR10
Submission date Jul 31, 2020
Last update date Apr 29, 2021
Contact name Sanchari Sircar
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
BioSample SAMN15689633
SRA SRX8860829

Supplementary file Size Download File type/resource
GSM4705369_HiChIP_Shoot_rep2_S6.allValidPairs.txt.gz 727.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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