16 rRNA amplicon of freshwater bacterioplankton - SRA

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SRX24884882: 16 rRNA amplicon of freshwater bacterioplankton
1 ILLUMINA (Illumina MiSeq) run: 36,393 spots, 18.3M bases, 11.9Mb downloads

Design: Initially, the full-length 16S rRNA gene was amplified using forward EUB8F and reverse 1492R primers (Table 1) with 10 ng of template DNA and high-fidelity SuperFi polymerase (Life Technologies) across 30 cycles of denaturation at 98C for 10 seconds, annealing at 50C for 45 seconds, and extension at 72C for 30 seconds. The PCR products were purified using the CleanPCR kit (CleanNA), according to the manufacturer's instructions, and DNA concentrations were determined with a Nanodrop spectrophotometer. A second amplification was then conducted on 10 ng of the purified PCR product using forward 515F and reverse 806R primer pair (Table 1) primer pair for 30 cycles, under the same thermal cycling conditions as before (Kozich et al., 2013)1. The second step PCR primers incorporated both an Illumina adapter sequence and an 8-nucleotide barcode at the 5' end for multiplex sequencing. The last PCR amplifications reactions were conducted in triplicate for each sample, pooled, and the correct size of the amplicon verified on a 1.5% agarose gel. The amplicons were purified using the CleanPCR kit (CleanNA) and sequenced on the Illumina MiSeq platform using a v2 PE500 kit producing 250-nt paired-end reads. To prepare an equimolar library for sequencing, amplicon concentrations were normalised using a SequalPrep Normalisation Plate (Applied Biosystems) and pooled accordingly.

Submitted by: KU Leuven

Study: Effects of Microplastics on Daphnia-Associated Microbiomes: A Combined In-Situ and In-Vitro Study

PRJNA1122644 • SRP513253 • All experiments • All runs

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The study aimed to investigate the effects of MP on the freshwater Daphnia-associated microbiome in a combined in-situ and in-vitro study.

Sample: Citadell bact pl HID3 2-7-21 100ML

SAMN41798753 • SRS21593458 • All experiments • All runs

Organism: freshwater metagenome

Library:

Name: N140

Instrument: Illumina MiSeq

Strategy: AMPLICON

Source: METAGENOMIC

Selection: PCR

Layout: PAIRED

Runs: 1 run, 36,393 spots, 18.3M bases, 11.9Mb

Run	# of Spots	# of Bases	Size	Published
SRR29370406	36,393	18.3M	11.9Mb	2024-06-12

ID:: 33219516

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