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Sample GSM4623384 Query DataSets for GSM4623384
Status Public on Nov 30, 2020
Title AK58_leaf_HiC_rep1
Sample type SRA
 
Source name AK58
Organism Triticum aestivum
Characteristics tissue: leaf
cultivar: AK58
Treatment protocol No treatment applied
Growth protocol Seeds were germinated and cultured with water in Petri dishes for 1 week, then transferred into nutrient solution cultured for another 2 weeks till three-leaf stage, in a growth chamber with 20 °C/18 °C (day/night), 16 h/8 h (light/dark). Leaves were harvested at 11:00 AM-12:00 PM
Extracted molecule genomic DNA
Extraction protocol Bisulfite and RNA sequencing samples were prepared with 2.2 μg DNA and 2μg total RNA (rRNA depleted) extracted from the harvested leaves respectively.
The library were constructed and the subsequent deep sequencing was completed by Novogene Co Ltd. For in situ HiC library, rep1 used HindIII enzyme and rep2 used DpnII enzyme.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina HiSeq 3000
 
Data processing Sequencing reads were cleaned with the Trim Galore (version 0.4.4), Trimmomatic (version 0.36) , and Sickle programs, which eliminated bases with low-quality scores (< 25), irregular GC contents, sequencing adapters, and short reads.
The cleaned reads were mapped to AK58 genome using Bismark_v0.19.0 for bisulfite-sequencing data, HISAT2(v2.1.0)for RNA-sequencing data, HiC-Pro(v2.11.1) for HiC-sequencing data.For smRNA-seq, cleaned reads of 24-nt were mapped to AK58 genome using Shortstack(v3.8.5)
Genome_build: AK58 genome
Supplementary_files_format_and_content: In RNA-seq, read counts for genes were provided;In smRNA-seq ,24nt-sRNA cluster files were provided; In Bisulfite-seq ,tdf files with position and methylation ratio were provided.
 
Submission date Jun 17, 2020
Last update date Dec 04, 2020
Contact name yijing zhang
E-mail(s) zhangyijing@fudan.edu.cn
Organization name Fudan University
Department Biochemistry
Lab Functional Epigenomics Group
Street address 2005 Songhu Road
City shanghai
ZIP/Postal code 200438
Country China
 
Platform ID GPL24354
Series (1)
GSE139020 Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression
Relations
BioSample SAMN15297855
SRA SRX8565923

Supplementary file Size Download File type/resource
GSM4623384_AK58_leaf_HiC_rep1_TADs.bed.gz 130.5 Kb (ftp)(http) BED
GSM4623384_AK58_leaf_HiC_rep1_loops.2D.bed.gz 418.8 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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