KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| PE/Cy7 anti-human CD62L | Biolegend | Clone: DREG-56; Cat# 304822 |
| APC anti-human CD45RA | Biolegend | Clone: HI100; Cat# 304112 |
| FITC anti-human CD8a | Biolegend | Clone: RPA-T8; Cat# 301050 |
| CD19-PerCP/Cy5.5 | Biolegend | Clone: HIB19; Cat# 302230 |
| PE anti-human CD38 | Biolegend | Clone: HB-7; Cat# 356604 |
| PE/Cy7 anti-human CD27 | Biolegend | Clone: O323; Cat# 302838 |
| FITC anti-human CD3 | Biolegend | Clone: OKT3; Cat# 317306 |
| FITC anti-human CD4 | Biolegend | Clone: RPA-T4; Cat# 300538 |
| PE anti-human CD4 | Biolegend | Clone: RPA-T4; Cat# 300508 |
| CD14-PerCP/Cy5.5 | Biolegend | Clone: HCD14; Cat# 325622 |
| CD16-PE | Biolegend | Clone: 3G8; Cat# 302008 |
| CD8-APC | Biolegend | Clone: HIT8a; Cat# 300912 |
| APC anti-human CD56 | Biolegend | Clone: NCAM; Cat# 318310 |
| FITC CD91 | BD Bioscience | Cat# 550496 |
| Biological samples | ||
| PBMC, whole blood and immune subpopulations | Healthy human donors in Genetic and Epigenetic Signatures of Translational Aging Laboratory Testing study (GESTALT) | https://www.clinicaltrials.gov/ct2/show/NCT02339012 |
| Chemicals | ||
| HBSS buffer | Mediatech | Part # 21-022-CM |
| Critical commercial assays and kits | ||
| Ficoll-Paque PLUS | GE Healthcare | Cat# GE17-1440-03 |
| 1X DPBS (Dulbecco's Phosphate Buffered Saline, DPBS) w/o Ca & Mg | Quality Biological | SKU# 114-057-131 |
| EasySep™ Human Monocyte Enrichment Kit without CD16 Depletion | STEMCELL Technologies | Cat# 19058 |
| EasySep™ Human Whole Blood CD66b Positive Selection Kit | STEMCELL Technologies | Cat# 18682 |
| EasySep Negative Human B Cell, Kit | STEMCELL Technologies | Cat# 19054 |
| EasySep Negative Human CD4 Kit | STEMCELL Technologies | Cat# 19052 |
| EasySep Negative Human CD8, Kit | STEMCELL Technologies | Cat# 19053 |
| Zymo EZ-96 DNA Methylation Kit | Zymo | Cat# D5003 |
| Infinium® MethylationEPIC BeadChip Kit | Illumina | Cat# WG-317-1003 |
| Single Read Flowcell - Big (v4 SR Cluster Kit) | Illumina | Cat# GD-401-4001 |
| Sequencing Reagent for Big Flowcell (v4 SBS HiSeq) (50 cycles) | Illumina | Cat# FC-401-4002 |
| TrueSeq ChIPSeq 48 samples (SetA) | Illumina | Cat# IP-202-1012 |
| TrueSeq ChIPSeq 48 samples (Set B) | Illumina | Cat# IP-202-1024 |
| RNeasy Mini Kit (250) | Qiagen | Cat# 74106 |
| miRNeasy mini kit | Qiagen | Cat# 217004 |
| Low Input RiboMinus™ Eukaryote System v2 | Life Technologies Corporation | Cat# A15027 |
| Bioanalyzer RNA 6000 Nano kit | Agilent | Part No.# 5067-1511 |
| Ovation RNASeq System Kits V2 | Nugen | Part No.# 7102-A01 |
| Deposited data | ||
| Methylation data | This paper | GEO: GSE184269 |
| RNASeq data | This paper | GEO: GSE184264 |
| EBF1 Chip-Seq data | This paper | GEO: GSE183537 |
| DNase-seq, H3K4me1,H3K4me3 and H3K27ac data | ENCODE project | https://www.encodeproject.org/ |
| 18 state model of immune cells | chromHMM | https://egg2.wustl.edu/roadmap/web_portal/chr_state_learning.html#exp_18state |
| Tejedor 850K methylation data | (Tejedor et al., 2018) | ArrayExpress Accession # E-MTAB-6315 |
| Softwares and algorithms | ||
| GenomeStudio 2011.1 | Illumina | https://www.illumina.com/techniques/microarrays/array-data-analysis-experimental-design/genomestudio.html |
| FlowJo v10 | FlowJo | https://www.flowjo.com |
| GraphPad Prism v8 | GraphPad Software | https://www.graphpad.com |
| R Studio 3.6.0 | The R Foundation | https://www.r-project.org |
| DESeq2 v1.30.1 | (Love et al., 2014) | DOI: 10.18129/B9.bioc.DESeq2 |
| minfi 1.38.0 | (Aryee et al., 2014) | DOI: 10.18129/B9.bioc.minfi |
| Methylation plotter | (Mallona et al., 2014) | https://gattaca.imppc.org/methylation_plotter/ |
| Cutadapt 3.4 | (Martin, 2011) | DOI:10.14806/ej.17.1.200 |
| FastQC 0.11.9 | (Andrews, 2010) | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| STAR Aligner 2.7.9a | (Dobin et al., 2013) | DOI: 10.1093/bioinformatics/bts635 |
| featureCounts v1.5.2 | (Liao et al., 2019) | DOI: 10.1093/bioinformatics/btt656 |
| ReactomePA 1.36.0 | (Yu and He, 2016) | DOI: 10.18129/B9.bioc.ReactomePA |
| ClusterProfiler 4.0.5 | (Yu et al., 2012) | DOI: 10.18129/B9.bioc.clusterProfiler |
| Deeptools 3.5.1 | (Ramirez et al., 2016) | DOI:10.1093/nar/gkw257 |
| Bedops 2.4.40 | (Neph et al., 2012) | DOI: 10.1093/bioinformatics/bts277 |
| HOMER 4.11.1 | (Heinz et al., 2010) | DOI: 10.1016/j.molcel.2010.05.004 |
| Other | ||
| DNA Isolation, DNAQuik DNA Extraction protocol | Reprocell | N/A |
| DNA Isolation, Qiagen DNeasy kit (for all cell types) | Genetic Resources Core Facility, Johns Hopkins University | N/A |
| DNA Isolation, Chemagic Chemistry on MSM I workstation (for WB) | Genetic Resources Core Facility, Johns Hopkins University | N/A |