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SRX19720219: DNA-Seq of BALF
1 ILLUMINA (NextSeq 550) run: 1.6M spots, 69.1M bases, 59.3Mb downloads

Design: Experienced clinicians guided the bronchoscopy to diseased region of the lungs referring to CT results. Sterile normal saline was instilled and then retrieved by gentle suction as BALF sample. Centrifuge the BALF samples at 1000 rpm for 10 min at 4 C and supernatants and precipitation were separately frozen (80 C) for further analysis. DNA was extracted from the precipitation using a QIAamp UCP Pathogen DNA Kit (Qiagen) following the manufacturer provided protocol. Human DNA was removed using Benzonase (Qiagen) and Tween20 (Sigma).10 nanograms DNA samples was used to construct library using Nextera XT DNA Library Prep Kit (Illumina, San Diego, CA). Library pools were then loaded onto an Illumina Nextseq 550Dx sequencer for 75 cycles of single-end sequencing to generate approximately 20 million reads for each library. Peripheral blood mononuclear cell samples with 105 cells/mL from healthy donors was served as negative controls. DNA-free water also went through DNA extraction and mNGS analysis as a blank control group to assess the degree of background contamination.
Submitted by: Shanghai Tenth People Hospital, Tongji University
Study: Microbiome in Lower Respiratory Tract of community-acquired pneumonia with or without COPD
show Abstracthide Abstract
Pulmonary physicians may choose a different empirical antibiotic therapy when faced with a community-acquired pneumonia(CAP) patient concomitant with chronic obstructive pulmonary disease(COPD) compared to a CAP patient without COPD. However, the detailed microbiome distribution in lower respiratory tract of CAP with COPD or CAP without COPD was unknown. So we used metagenomic next generation sequencing(mNGS) to explore the microbiome differences between the two groups.
Sample: missing
SAMN33820086 • SRS17087142 • All experiments • All runs
Library:
Name: 19S0078649
Instrument: NextSeq 550
Strategy: WGS
Source: METAGENOMIC
Selection: unspecified
Layout: SINGLE
Runs: 1 run, 1.6M spots, 69.1M bases, 59.3Mb
Run# of Spots# of BasesSizePublished
SRR239087021,607,08069.1M59.3Mb2023-08-30

ID:
27030731

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