Illumina paired-end sequencing

Knowledge graph centered on Illumina paired-end sequencing with 75 nodes and 182 connections. Top connected: Bacteria, snowpack persistence, leaf water content, Virus diversity and activity is driven by snowmelt, carbon cycling.

Method synopsis

Standard Illumina library preparation using Nextera XT kit followed by paired-end sequencing on HiSeq 2500 platform to generate comprehensive metagenomic datasets from phylloplane microbial communities.

Synthesized from method descriptions across 4 papers using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome (2025), Microbiome. The protocol was originally introduced by Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale (2021), Microbiome. Implementations in other papers (listed below) may differ.

1. Illumina library preparation
   Libraries prepared using standard JGI protocols following protocols described in reference [12]. Nextera XT kit used with 2 ng of DNA fragmented and adapter ligated. Ligated DNA fragments were PCR amplified and purified using SPRI beads
   Quantities: 2 ng DNA input per library, 67 libraries totalDuration: Standard library prep timeframeConditions: Following JGI standard protocols
   Equipment: Nextera XT kit, SPRI beads, Beckman Coulter, LightCycler 480 real-time PCR instrument, Roche
2. High-throughput sequencing
   Sequencing performed on HiSeq 2500 platform generating 150 bp paired-end reads
   Quantities: 150 bp paired-end reads, 67 metagenomes sequencedDuration: Standard HiSeq run timeConditions: Illumina HiSeq 2500 platform specifications
   Equipment: HiSeq 2500

Typical Equipment

• Nextera XT kit
• SPRI beads
• Beckman Coulter
• LightCycler 480 real-time PCR instrument
• HiSeq 2500

Output Measurements

• 150 bp paired-end metagenomic reads

Papers Using This Protocol (5)

Species Studied With This Protocol

Places Where Used