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Sample GSM6077013 Query DataSets for GSM6077013
Status Public on Aug 09, 2022
Title Hi-C_ndx1-4_rep2
Sample type SRA
Source name 10-day-old seedling
Organism Arabidopsis thaliana
Characteristics tissue: Seedling
age: 10 days
genotype: ndx1-4
Growth protocol 2 g of 10-day-old seedlings of Col-0, and ndx1-4 plants were harvested.
Extracted molecule genomic DNA
Extraction protocol Hi-C experiments were performed by the Arima HiC Kit (Arima Genomics). 10-day-old Columbia wild type (Col-0) and ndx1-4 seedlings were crosslinked with 1% formaldehyde. According to the Arima User Guide for Plant tissue (, 1 g of crosslinked plant tissue was used as a starting material for isolation of nuclei. Plant samples were ground in liquid nitrogen using a mortar. 20 ml of PTNI buffer was then added (250 mM Sucrose, 20 mM HEPES pH 8.0, 5 mM KCl, 1mM MgCl2, 40% glycerol, 0.1 mM PMSF, 1% protease inhibitor cocktail (Sigma), 0.25% Triton X-100, 0.1% mercaptoethanol) and samples were purified two times by using a double-layer Mirachlot (Merk). Nuclei were washed several times in PTNI buffer as described in the Arima-HiC User Guide.
Proximity ligated in situ Hi-C libraries were then constructed according to the Arima User Guide. Hi-C samples were fragmented to an average size of 400 bp (Bioruptor UCD-300, Diagenode; low intensity mode, 3 x 5 min; 30 sec ON, 30 sec OFF). NGS libraries for Illumina sequencing were prepared using the Accel-NGS 2S Plus DNA Library Kit and Accel-NGS 2S Indexing Kit (Swift Biosciences). To estimate the proper number of PCR cycles for library amplification, Arima-QC2 values were determined using the KAPA Library Quantification Kit (Roche). NGS library amplifications were performed until the estimated PCR cycle numbers (usually between 5-9) using the Kapa Library Amplification Kit (Roche). NGS libraries were then sequenced on an Illumina NextSeq 500 platform (2x150 nt, paired end reads) using a NextSeq 500 High Output v2 kit (Illumina).
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Description A. thaliana reference genome (TAIR10)
ndx1-4 mutant 10-day-old seedling.
Paired-end Hi-C; reads1 and reads2 in different raw files; replica 2.
Data processing Raw Hi-C libraries (.fastq files) were processed by the Juicer toolbox using default parameters, except that appropriate restriction enzyme cutting sites - provided by the Arima-HiC kit (GATC and GANTC) - were introduced into the script files. Hi-C reads were mapped to the A. thaliana TAIR10 reference genome and MAPQ>=30 reads were retained for further analysis.
Quantitative differences in Hi-C interactions (Col-0 (wild type) vs. ndx1-4 mutant) were identified at 25 kb resolution by the Slitherine pipeline ( Slitherine runs the Serpentine tool to smooth local noise in Hi-C interaction maps and identifies statistically significant differences between Hi-C contact matrices.
Assembly: A. thaliana reference genome (TAIR10; NCBI; Ecotype: Columbia-0).
Supplementary files format and content: Hi-C data (hic files) are from col0 and ndx1-4 (two replicas) samples.
Supplementary files format and content: Quantitative differences (tsv file) in Hi-C interactions (Col-0 (wild type) vs. ndx1-4 mutant) were identified at 25 kb resolution by the Slitherine pipeline.
Submission date Apr 28, 2022
Last update date Aug 09, 2022
Contact name Márton Miskei
Organization name University of Debrecen
Department Department of Biochemistry and Molecular Biology
Street address Nagyerdei Krt. 48.
City Debrecen
ZIP/Postal code 4032
Country Hungary
Platform ID GPL19580
Series (2)
GSE201839 Nodulin homeobox (NDX) is required for heterochromatin homeostasis in Arabidopsis [Hi-C]
GSE201841 Nodulin homeobox (NDX) is required for heterochromatin homeostasis in Arabidopsis
BioSample SAMN27963117
SRA SRX15045437

Supplementary file Size Download File type/resource
GSM6077013_at_hic_ndx1-4_r2.hic 799.8 Mb (ftp)(http) HIC
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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