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Sample GSM3929163 Query DataSets for GSM3929163
Status Public on Mar 02, 2020
Title Wheat.shoot.Hi-C
Sample type SRA
 
Source name Shoot
Organism Triticum aestivum
Characteristics genotype: Chinese Spring
developmental stage: 14 days old seedlings
tissue: shoot
Growth protocol Seeds were surface sterilized with bayrochlore and ethanol, sown on MS agar plates, placed at 4°C in the dark for 2 days and then grown in a growth chamber for 14 days (long day conditions, 18°C).
Extracted molecule genomic DNA
Extraction protocol The experiment was carried out according to the protocol published by Liu et al., 2017 using DpnII enzyme (New England Biolabs) with minor modifications concerning library preparation for which we used NebNext UltraII DNA library preparation kit (New England Biolabs).
For library amplification, nine PCR cycles were performed and Hi-C libraries were purified with SPRI magnetic beads (Beckman Coulter) and eluted in 20 μL of nuclease-free water. The quality of the libraries was assessed with Agilent 2100 Bioanalyzer (Agilent)
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Data processing Short-reads were trimmed with the following command "trimmomatic-0.36.jar PE -phred33 -validatePairs ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:20"
Trimmed short-reads were processed with the pipeline HiC-Pro v2.9.0 (Servant N. et al., 2015) with minor modifications. Briefly, reads were aligned to iwgsc_refseq1.0 reference genome assembly using bowtie2 v2.3.3 (60) with default settings, except for the parameter “--score-min L,-0.6,-0.8”. Forward and reverse mapped reads were paired and assigned to MboI restriction fragments. Invalid ligation products (such as dangling ends, fragments ligated on themselves and ligations of juxtaposed fragments) were discarded to identify valid pairs. Valid pairs of each sample were merged and used to produce raw interaction matrixes at various resolution as part of HiC-Pro pipeline. Normalized matrixes were produced by iterative correction using the “ice” utility provided as part of HiC-Pro (Imakaev et al., 2012).
Insulation index was calculated from 25-kb ice-normalized matrixes using tadtool v0.77 with the command "tadtool tads -a ninsulation --write-values MATRIX MATRIX.BED 100000 0.4 > INSULATION_INDEX"
Genome_build: iwgsc_1.0
Supplementary_files_format_and_content: ValidPairs identified by HiC-Pro are stored using a simple tab-delimited text format: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]. Insulation index obtained with TADtool v0.7.7 is stored as bigwig file
 
Submission date Jul 05, 2019
Last update date Mar 02, 2020
Contact name Lorenzo Concia
E-mail(s) colore@gmail.com, concia@bio.ens.psl.eu
Phone 769929568
Organization name École Normale Supérieure
Department Institut de Biologie
Lab Plant and Algal Genomics Lab
Street address 46 Rue d'Ulm
City Paris
ZIP/Postal code 75020
Country France
 
Platform ID GPL23509
Series (2)
GSE133882 Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat_Hi-C)
GSE133885 Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories
Relations
BioSample SAMN12219942
SRA SRX6408588

Supplementary file Size Download File type/resource
GSM3929163_Wheat.shoot.25000_iced.win_100kb.nins_index.bigwig 8.3 Mb (ftp)(http) BIGWIG
GSM3929163_Wheat.shoot.hicpro.allValidPairs.txt.gz 32.2 Gb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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