AMPLICON of skin: large plaque psoriasis - SRA

SRX15182763: AMPLICON of skin: large plaque psoriasis
1 ILLUMINA (Illumina MiSeq) run: 38,886 spots, 16.5M bases, 7.2Mb downloads

Design: Polymerase chain reaction (PCR) amplification of target gene was performed using general primers V3-V4. The primers also contained the Illumina 5'overhang adapter sequences for two-step amplicon library building, following manufacturer's instructions for the overhang sequences. The initial PCR reactions were carried out in 50 L reaction volumes with 1-2 L DNA template, 200 uM dNTPs, 0.2 uM of each primer, 5X reaction buffer 10uL and 1U Phusion DNA Polymerase (New England Biolabs, USA). PCR conditions consisted of initial denaturation at 94 C for 2 min, followed by 25 cycles of denaturation at 94 C for 30 s, annealing at 56 C for 30 s and extension at 72 C for 30 s, with a final extension of 72 C for 5 min. The second step PCR with dual 8-base barcodes was used for multiplexing. Eight cycle PCR reactions were used to incorporate two unique barcodes to either end of the 16S amplicons. Cycling conditions consisted of one cycle of 94 C for 3 min, followed by eight cycles of 94 C for 30 s, 56 C for 30 s and 72 C for 30 s, followed by a final extension cycle of 72 C for 5 min. Prior to library pooling, the barcoded PCR products were purified using a DNA gel extraction kit (Axygen, USA) and quantified using the FTC -3000 TM real-time PCRFunglyn Shanghai. The PCR products from different samples were indexed and mixed at equal ratios for sequencing on the illumina platform at TinyGen Bio-Tech (Shanghai) Co., Ltd.

Submitted by: Xiangya hospital, Central South University

Study: Microbiota differences between patients with plaque and guttate psoriasis

PRJNA835606 • SRP373885 • All experiments • All runs

show Abstracthide Abstract

Psoriasis can be provoked or exacerbated by environmental exposures such as certain microbiomes. The distinction between plaque psoriasis (PP) and guttate psoriasis (GP) in the skin or pharyngeal microbiota is not yet clear. High-throughput sequencing using Illumina MiSeq was used in this study to characterize skin and pharyngeal microbial composition in patients with PP (large PP (PP, n=62), small PP (SPP, n=41)) and GP (n=14). The alpha and beta diversity of skin microbiota LPP was similar to that of the SPP group, but different from the GP group. There were no differences in pharyngeal microbiota among the groups. According to LEfSe analysis, Staphylococcus, Stenotrophomonas, Enhydrobacter, Brevundimonas, and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium were the dominant genera of skin microbiota in PP. Diversity of skin microbiota correlated with Psoriasis Area and Severity Index (PASI). Moderate-to-severe psoriasis and mild psoriasis have different microbiota compositions. The skin microbiota may be related to the pharyngeal microbiota. Furthermore, two microbiota models could distinguish psoriasis subtypes with ROC-AUC of 0.935 and 0.836, respectively. In conclusion, the skin microbiota in patients with LPP is similar to that in patients with SPP, but displays variations compared to that of GP, no differences are noted between subtypes in pharyngeal microbiota. Skin microbiota diversity correlated with PASI.

Sample:

SAMN28105428 • SRS12923502 • All experiments • All runs

Organism: Acinetobacter lwoffii

Library:

Name: I02.138LPPp

Instrument: Illumina MiSeq

Strategy: AMPLICON

Source: METAGENOMIC

Selection: PCR

Layout: SINGLE

Runs: 1 run, 38,886 spots, 16.5M bases, 7.2Mb

Run	# of Spots	# of Bases	Size	Published
SRR19115058	38,886	16.5M	7.2Mb	2022-07-27

ID:: 21660722

SRA

Sequence Read Archive

Result Filters

Send to:

Supplemental Content

Related information

Recent activity