Comparison of Brain Epigenetic Maps in Cross-Disorder RNAseq Analysis

Capstone Projects Cross-disorder analysis - RNAseq Adult and Disease - Epigenetic map Development Comparison with ENCODE, GTEX and ROADMAP 1

Human Studies Study Assay Assay Target Individuals Samples Disorder Tissue Dorsolateral Prefrontal Cortex Dorsolateral Prefrontal Cortex, Anterior Cingulate Cortex Dorsolateral Prefrontal Cortex Cell Type Data types WGBS-Pilot WGBS 1 3 Control tissue homogenate fastq, metRatio EpiMap ChIP-seq H3K4me3, H3K27ac 17 122 Control NeuN+, NeuN- bam, bed, bigwig Schizophrenia, Bipolar Disorder, Control Schizophrenia, Bipolar Disorder, Control HumanFC ATAC-seq 11 12 tissue homogenate bam, bed, bigwig BrainGVEX RNA-seq 220 229 Frontal Cortex tissue homogenate bam, fpkm GABA Neurons, GLU Neurons GABA Neurons, GLU Neurons fastq, differential methylation fastq, differential expression EpiGABA ERRBS 3 6 Control Orbitofrontal Cortex EpiGABA RNA-seq 2 4 Control Orbitofrontal Cortex Dorsolateral Prefrontal Cortex lncRNA-Pilot IsoSeq 1 4 Control tissue homogenate fastq, bed lncRNA-Pilot RNA-seq 2 cell lines 8 SH-SY5Y, A549 bam Cerebellum, Prefrontal Cortex, Temporal Cortex Cerebellum, Prefrontal Cortex, Temporal Cortex Autism Spectrum Disorder, Control UCLA-ASD RNA-seq 79 205 tissue homogenate fastq Autism Spectrum Disorder, Control UCLA-ASD ChIP-seq H3K27ac 111 285 tissue homogenate bam H3K27ac, H3K4me3, H3K4me1, CTCF Schizophrenia, ControlOlfactory CNON ChIP-seq 4 15 CNON fastq, bam, bed, bigwig Neuroepithelium Cerebellum, Dorsolateral Prefrontal Cortex Yale-ASD ChIP-seq H3K27ac 9 18 Control tissue homogenate ChIP-enriched regions iPSC derived organoids from 2 fetal and 1 adult individual, undifferentiated iPSC from 4 fetal and 2 adult individuals iPSC RNA-seq 31 Organoids iPSC, NeuN+, NeuN- bam 2

Animal Models Study Species Assay Animals Samples Treatment Tissue Cell Type haloperid ol, placebo tissue homogen ate MouseHA L Mus musculus ATAC-seq 14 14 Striatum bam, bed, bigwig Cerebellu m, Dorsolater al Prefrontal Cortex, Striatum tissue homogen ate Rhesus macaque NHP RNA-seq 3 9 bam 3

Projects generating brain NGS datasets Website Link Project name Organism Disease or control Brain region Datasets Control, biopolar disorder, schizophrenia, Autism spectrum disorder Homo sapiens, Rhesus macaque DFC,CBC,ACC,STR, HIP,AMY RNA-Seq, ChIP-Seq,DNase-seq, ATAC-seq,DNase- seq,WGBS,NOMe-seq http://psych encode.org/ PsychENCODE http://comm onmind.org/ WP/ Control, biopolar disorder, schizophrenia CommonMind Homo sapiens DFC, CBC, STG RNA-seq, ChIP-Seq, WGS, ATAC-Seq ADHD, autism, bipolar disorder, major depressive disorder, and schizophrenia https://www. med.unc.ed u/pgc Psychiatric Genomics Consortium (PGC) Homo sapiens N/A SNPs, CNVs https://www. nia.nih.gov/ alzheimers/ amp- ad#amp-ad Homo sapiens, iPSC,Mus musculus AMP Alzheimer s disease Knowledge Control, Alzheimer's Disease 19 brain regions RNA-Seq, ChIP-Seq, DNA Methylation http://grasp. nhlbi.nih.go v/Overview. aspx Genome-wide association studies (GWAS) Homo sapiens all kinds of disorders N/A SNPs http://brains pan.org/ Brainspan Homo sapiens Control 16 brain regions RNA-Seq, ChIP-Seq,Microarray, Methylation, MRI/DTI http://www.r oadmapepi genomics.or g/ http://www.g texportal.or g/home/ 9 brain regions and cultured cells Roadmap Epigenomics Mapping Consortium (Roadmap) Homo sapiens Control ChIP-Seq, DNase , DNA methylation, RNA-Seq The Genotype-Tissue Expression (GTEx) project Homo sapiens Control 13 brain regions RNA-Seq, eQTLs 4

Roadmap Epigenomics Mapping Consortium The NIH Roadmap Epigenomics Mapping Consortium was launched with the goal of producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. Collection of normal epigenomes that will provide a framework or reference for comparison and integration within a broad array of future studies. http://www.ncbi.nlm.nih.gov/epigenomics 5

The Genotype - Tissue Expression (GTEx) Project The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. 6