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Sample GSM3929166 Query DataSets for GSM3929166
Status Public on Mar 02, 2020
Title Wheat.root.Hi-ChIP
Sample type SRA
 
Source name Root
Organism Triticum aestivum
Characteristics genotype: Chinese Spring
developmental stage: 14 days old seedlings
tissue: root
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 Nuclei were isolated using the same procedure published by Liu et al., 2017. We then applied the HiChIP protocol of Mumbach et al., 2016 using the DpnII restriction enzyme (New England Biolabs) and anti-Polymerase II antibody (Active Motif, 39097).
The sequencing library was built according to the protocol of Mumbach et al, 2016. The quality of the libraries was assessed with Agilent 2100 Bioanalyzer (Agilent).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Library strategy: HiChiP
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 default settings. Briefly, reads were aligned to iwgsc_refseq1.0 reference genome assembly using bowtie2 v2.3.3. 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).
Genome_build: iwgsc_1.0
 
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 GPL26889
Series (2)
GSE133883 Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat Hi-ChIP)
GSE133885 Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories
Relations
BioSample SAMN12219939
SRA SRX6408591

Supplementary file Size Download File type/resource
GSM3929166_Wheat.root.HiChIP_RNAPII.hicpro.allValidPairs.txt.gz 3.7 Gb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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