WGBS of Populus nigra: Dranse_DRA-038 - SRA

SRX15807664: WGBS of Populus nigra: Dranse_DRA-038
1 ILLUMINA (Illumina HiSeq 4000) run: 135.6M spots, 41G bases, 16.7Gb downloads

Design: Whole genome bisulfite sequencing was performed using the Ovation Ultralow Methyl-seq kit (Tecan Genomics/ Nugen, San Carlos, CA, USA, http://www.nugen.com/products/ovation-ultralow-methyl-seq-library-systems) as indicated in Daviaud et al. (2018). The workflow of the library preparation protocol follows the classical library preparation protocol, in which methylated adaptors are ligated to the fragmented DNA prior to bisulfite conversion. Briefly, 200 ng of genomic DNA was fragmented to approximately 200 base pairs (bp) using a Covaris ultrasonicator (Woburn, Massachusetts, USA). The purified and methylated adaptors compatible with sequencing on an Illumina HiSeq instrument were the ligated. The resulting DNA library was purified and bisulfite converted. A qPCR assay was performed to determine the optimal number of PCR amplification cycles (between 10 to 15 cycles) required to obtain a high diversity library with minimal duplicate reads prior to the actual library amplification. The twelve samples to be sequenced were combined at equimolar concentrations in a single pool and the sequencing was performed in paired ends (2 x 150 pb) on four lanes of an Illumina HiSeq4000 flow-cell to a minimal theoretical coverage of 30 X for each sample.

Submitted by: INRAE - UMR BioForA

Study: Populus nigra Whole Genome Bisulfite Sequencing - Epigenomics

PRJNA828400 • SRP382876 • All experiments • All runs

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This project is part of the EPITREE ANR Research Project. It aims a studying the impact of poplar epigenetics (DNA methylation) in tree adaptation mechanisms to the local environment for one Populus species (P. nigra).

Sample:

SAMN27655102 • SRS12681244 • All experiments • All runs

Organism: Populus nigra

Library:

Name: B00J711_Dranse_DRA-038_13_WGBS

Instrument: Illumina HiSeq 4000

Strategy: Bisulfite-Seq

Source: GENOMIC

Selection: RANDOM

Layout: PAIRED

Runs: 1 run, 135.6M spots, 41G bases, 16.7Gb

Run	# of Spots	# of Bases	Size	Published
SRR19762976	135,638,649	41G	16.7Gb	2024-06-20

ID:: 22461828

SRA

Sequence Read Archive

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