NYU Data Catalog

Description

Psychological stress is linked with systemic inflammation. It accelerates inflammatory disease progression and monocytes are key in sustaining systemic inflammation. However, the mechanisms underlying stress-mediated inflammation and future health risk remains unknown. This study examined the impact of psychological stress on monocytes and showed that psychological stress induces remodeling of the chromatin landscape and transcriptomic reprogramming of monocytes. The dataset contains RNA and ATAC sequencing data. It includes RNA and ATAC sequencing of isolated bone marrow monoctyes from stressed and control mice. In addition, RNA sequencing of isolated bone marrow monocytes stimulated with lipopolysaccharide from stressed and control mice and isolated whole blood monocytes from humans with high and low stress.

Subject of Study
Homo sapiens
C57BL/6 mice
Subject Domain
Genomics
Keywords
Atherosclerosis
Cytokines
DNA
Genes
Genomics
Inflammation
Mitochondria
Monocytes
Myeloid Cells
Proteins
RNA
RNA Sequencing

Access

Restrictions
Free to All
Instructions
RNA and ATAC sequencing data have been deposited at the Gene Expression Omnibus (GEO).
Access via GEO


Accession #: GSE167536

Associated Publications
Barrett TJ, Corr EM, van Solingen C, Schlamp F, Brown EJ, Koelwyn GJ, Lee AH, Shanley LC, Spruill TM, Bozal F, de Jong A, Newman AAC, Drenkova K, Silvestro M, Ramkhelawon B, Reynolds HR, Hochman JS, Nahrendorf M, Swirski FK, Fisher EA, Berger JS, Moore KJ. Chronic stress primes innate immune responses in mice and humans. Cell Rep. 2021 Sep 7;36(10):109595.
Data Type
Biospecimens
Genomic
Equipment Used
Agilent 2100 Bioanalyzer

DNA, RNA, protein and cell analyzer

Applied Biosystems QuantStudio 3

Real-time PCR system

HESKA Element HT5

Hematology analyzer

Illumina HiSeq 2500

Sequencing system

Illumina HiSeq 4000

Sequencing system

Software Used
basepair

Next generation sequencing data analysis

bcl2fastq v2.20

Converts BCL to FASTQ format

biomaRt v2.40.5

Interface to BioMart databases

Bowtie2 v2.3.4.1

Fast and sensitive gapped read aligner

clusterProfiler

Tool for interpreting omics data

deepTools v2.3.3

Tools for exploring deep-sequencing data

DESeq2 v1.24.0

Differential gene expression analysis

DiffBind v3.3.0

Differential binding analysis of ChIP-seq peak data

FastQC v0.11.7

Tool for high throughput sequencing data

fastx_trimmer v0.0.13

Trims N nucleotides from end of sequences

featureCounts v1.6.3

Counts reads by genomic features

ggplot2 v3.3.3

System for creating graphics

GO Enrichment Analysis

Performs enrichment analysis on gene sets

GraphPad Prism v8.0

Statistical analysis

GREAT

Predicts functions of cis-regulatory regions

Ingenuity Pathway Analysis

Omics data analysis software

Integrative Genomics Viewer v2.5.2

Tool for visual exploration of genomic data

MACS

Model-based analysis for ChIP-seq

NucleoATAC

Nucleosome calling using ATAC-seq

pheatmap v1.0.12

Offers control over dimensions and appearance

Python v2.7.3

Programming language

R v4.0.2

Software for statistical computing and graphics

Revigo

Summarizes and visualizes long lists of gene ontology terms

RStudio v1.3.1093

Data visualization

Sambamba v0.6.7

Tool for extracting information from SAM/BAM files

STAR v2.6.1d

Fast RNA-seq read mapper

Trimmomatic v0.36

Flexible read trimming tool

Grant Support
R01 HL084312/NHLBI NIH
19CDA34630066/American Heart Association
R35 HL135799/NHLBI NIH
P01 HL131478/NHLBI NIH
T32 HL098129/NHLBI NIH
16SFRN28730002/American Heart Association
118CDA34110203/American Heart Association
18-A0-00-1001884/American Society of Hematology
R35 HL144993/NHLBI NIH