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Sample GSM4705373 Query DataSets for GSM4705373
Status Public on Apr 29, 2021
Title Capture_HiC_Col0_Root_rep2
Sample type SRA
 
Source name Capture_HiC_Col0_Root_rep2
Organism Arabidopsis thaliana
Characteristics genotype: Col0
Growth protocol Capture Hi-C libraries were performed on shoot and root of Col-0, ref6, and clf
Extracted molecule genomic DNA
Extraction protocol For capture Hi-C, in situ HiC libraries were first generated as in Concia et al., 2020. Capture was then performed using SureSelect XT Target Enrichment System for Illumina Paired-End Multiplexed Sequencing Library (Agilent) according to manufacturer’s recommendation.
Libraries were performed according to SureSelect XT Target Enrichment System for Illumina Paired-End Multiplexed Sequencing Library (Agilent) according to manufacturer’s recommendation.
Capture Hi-C libraries
 
Library strategy Hi-C
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
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 SAMN15689629
SRA SRX8860833

Supplementary file Size Download File type/resource
GSM4705373_CHiC_Col_Root_rep2_S5.allValidPairs.txt.gz 342.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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