Reduced representation bisulfite sequencing of WWB-1146: whole blood ... - SRA

SRX24268206: Reduced representation bisulfite sequencing of WWB-1146: whole blood sample
1 ILLUMINA (Illumina NovaSeq 6000) run: 3.2M spots, 686.3M bases, 235Mb downloads

Design: Genomic DNA was extracted and purified from 200 L of whole blood samples using Monarch Genomic DNA Purification Kits (New England Biolabs, United Kingdom). Samples of ~200 ng genomic DNA were digested with 20 units of MspI (C*CGG) and 10 units of AluI (AG*CT) (New England Biolabs, United Kingdom) at 37C overnight (~16 hours). Digested DNA was purified using 1.8 AMPureXP magnetic beads (Agencourt, United States), then end-prepped and dA-tailed using the NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs, United Kingdom). Methylated adaptors were ligated to the end-repaired and dA-tailed DNA using the NEBNext Ultra II Ligation Module (New England Biolabs, United Kingdom), followed by USER enzymatic treatment. Ligated products were purified and size-selected for fragments shorter than 450 bp using 0.6 AMPureXP. Size-selected fragments were bisulfite-converted using Methylamp One-Step DNA Modification Kit (Epigentek, United States) according to the manufacturers protocol. These sub-libraries were barcoded and enriched using NEBNext Q5U Master Mix (New England Biolabs, United Kingdom). Sub-libraries were purified using 1.8 AMPureXP and pooled to equimolarity for the final library at ~20 nM, which was then sequenced on an Illumina NovaSeq 6000 system with paired-end mode of 150 bp.

Submitted by: University of Oxford

Study: Reduced representation bisulfite sequencing of Meles meles

PRJNA1100394 • SRP501895 • All experiments • All runs

show Abstracthide Abstract

Adversity experienced in early life can cause permament changes in individual phenotypes through epigenetic modification, such as DNA methylation. There is particularly a growing interest how prenatal conditions can exert developing stress on phenotypes. In this project, we utilised blood samples from a natural population of European badgers (Meles meles) studied systemtically at Wytham Woods for more than 30 years and analysed methylation patterns in ~4-month-old 95 individuals between 2003 and 2011 using reduced representation bisulfite sequencing.

Sample: Reduced representation bisulfite sequencing of WWB-1146

SAMN40969059 • SRS21034484 • All experiments • All runs

Organism: Meles meles

Library:

Name: WWB-1146_RRBS

Instrument: Illumina NovaSeq 6000

Strategy: Bisulfite-Seq

Source: GENOMIC

Selection: Reduced Representation

Layout: PAIRED

Runs: 1 run, 3.2M spots, 686.3M bases, 235Mb

Run	# of Spots	# of Bases	Size	Published
SRR28700436	3,197,579	686.3M	235Mb	2024-07-07

ID:: 32580733

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