Strain-specific alterations in gut microbiome and host immune responses elicited by tolerogenic Bifidobacterium pseudolongum

UMB Dataset

Access via GenBank

genomes, metagenome, and transcriptome sequences
Accession #: PRJNA809764

Access via GitHub

R codes and input dataset

Access via Article

Immunologic experimental raw data files

Accu-Scope EXC-500

Provides sharp, crisp images via Plan achromat or Plan semi-Apochromatic objectives.

Anaerobic microplates

Rapid broad-based identification and characterization product designed for anaerobic bacteria.

Bifido Selective Media agar plates

For the selective isolation and identification of Bifidobacteria.

BioAnalyzer 2100

Automated electrophoresis tool for the sample quality control of biomolecules

CD11c positive selection kit

Magnetic separation of CD11c+ cells by positive selection.

DNA/RNA Shield

DNA and RNA stabilization solution for nucleic acids in any biological sample.

GasPak EZ

Generates a pouch-based anaerobic, microaerophilic or CO2-enriched environment.

Illumina MiSeq System

Capable of automated paired end reads.

Illumina NovaSeq 6000 Sequencing System

Performs whole-genome sequencing

KAPA Hyper Prep kit KK8504

LSRFortessa Flow Cytometer

Multicolor analysis with powerful fluidics systems and novel optics design to maximize signal and enable minimum cross talk.

Microm HM550

Cryostats for sectioning techniques in routine and research.

Nextera XT Flex kit

Prepare sequencing libraries for small genomes, PCR amplicons, plasmids, or cDNA

Phasemaker tubes

A thick liquid polymer that separates and completely isolates the upper aqueous phase of a TRIzol Reagent mix from the organic phase underneath, greatly simplifying removal of the upper phase containing the RNA.

Promega Wizard Genomic DNA Purification Kit

A reliable and widely used kit designed for efficient extraction and purification of high-quality genomic DNA from various biological samples.

RiboZero Plus kit

Removes abundant RNA using enzymatic depletion.

RNA 1000 Nano kit

Provides reliable and reproducible characterization of total RNA and mRNA from multiple sample types.

RNAlater

Immediate RNase inactivation and stabilization of RNA in tissues, cultures of Gram-positive and Gram-negative bacteria and sorted or cultured cells to preserve the gene expression profile and enable reproducible purification of high-quality RNA.

Spectrophotometer microplate reader

Run standard spectrophotometer and microplate reader applications.

TRIzol Reagent

A complete, ready-to-use reagent for the isolation of high-quality total RNA or the simultaneous isolation of RNA, DNA, and protein from a variety of biological samples

TruSeq Stranded mRNA

Prepare sequencing libraries from mRNA to get a clear view of the coding transcriptome with strand-specific information.

UV CrossLinker

Quick, safe, and efficient sample exposure to a controlled amount of UV radiation.

anvi'o pangenome pipeline

Advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies.

anvi'o vers 6.2 workflow

Open source software analysis and visualization platform for microbial genomics.

BMTagger

A tool that discriminates between human reads and microbial reads without performing an alignment of all reads to the human genome.

Braken

Highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

clusterProfiler Bioconductor package

Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters.

Cnetplot function

Used as a general method to visualize data relationships in a network diagram.

dbCAN2

Web server for automated Carbohydrate-active enzyme Annotation.

DESeq

Differential gene expression analysis based on the negative binomial distribution

eggNOG-mapper v2

Software tool for functional annotation of large sets of sequences.

enrichGO

Given a vector of genes, this function will return the enrichment GO categories after FDR control.

fastp

Software tool to provide fast all in one preprocessing for FastQ files

FastQC

Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines.

FlowJo

Software for single-cell flow cytometry analysis. Its functions include management, display, manipulation, analysis and publication of the data stream produced by flow and mass cytometers.

Gene Ontology enrichment analysis

Performs enrichment analysis on gene sets.

GhostKOALA

Assigns K numbers to the user's sequence data by GHOSTX search against a nonredundant set of KEGG GENES.

HiSat

Graph-based alignment of next generation sequencing reads to a population of genomes.

HTSeq

Analysing high-throughput sequencing data with Python

HUMAnN2

A pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data.

Kraken2

A set of software tools designed to streamline the analysis of next-generation sequencing data.

MAUVE Contig Mover

Used to order a draft genome relative to a related reference genome.

MUSCLE

Software for multiple sequence alignment, used to align protein or nucleotide sequences for comparative analysis.

Pfam vers34.0

A database of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).

phyloseq

Software for handling and analysis of high-throughput microbiome census data.

PSORTb

Precise bacterial localization prediction tool.

SoftMax Pro 7

A software package for microplate reader control and microplate data analysis.

Sourmash v. 3.3

Software library for sketching of DNAsearch. Used to compare and analyze genomic and metagenomic data sets.

SPAdes

vegan package

Ordination methods, diversity analysis and other functions.

Volocity 3D Image Analysis Software

3D image analysis software to visualize, analyze and validate 3D fluorescence images.

Observational

Markov Cluster Algorithm

Hidden Markov model

Rao score test

Linear discriminant analysis Effect Size

Kruskal-Wallis

Latent Dirichlet Allocation model

Canonical Correspondence Analysis

polymerase chain reaction assay

Over-representation analyses