NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
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 (https://arimagenomics.com/), 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 (https://gitlab.pasteur.fr/gmillot/slitherine). 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
E-mail(s) miskeim@gmail.com
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
Relations
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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap