|
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 |