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ENCODE Search the ENCODE Portal ENCODE SCREEN Functional genomics Functional characterization Encyclopedia of elements Rush Alzheimer’s EN-TEx Deeply profiled cell lines Protein knockdown (Degron) Computational and integrative products Human donors ENCORE Stem cell differentiation Imputed experiments
ENCODE Encyclopedia, Version 4: Genomic annotations – ENCODE The ENCODE Encyclopedia organizes the most salient analysis products into annotations and provides tools to search and visualize them The Encyclopedia has two levels of annotations: Integrative-level annotations integrate multiple types of experimental data and ground level annotations
Getting Started - ENCODE Welcome to the ENCODE Portal! The ENCODE Portal, developed and maintained by the Data Coordination Center (ENCODE DCC), is the canonical source for all experimental metadata and data from ENCODE and associated projects
publications – ENCODE The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10 5 days after conception until birth, including transcriptomes, methylomes and chromatin states
ATAC-seq Data Standards and Processing Pipeline - ENCODE The ENCODE ATAC-seq pipeline is used for quality control and statistical signal processing of short-read sequencing data, producing alignments and measures of enrichment Pipeline schematic for replicated data
SCREEN: Search Candidate Regulatory Elements by ENCODE SCREEN is a web interface for searching and visualizing the Registry of candidate cis-Regulatory Elements (cCREs) derived from ENCODE data The Registry contains 1,063,878 human cCREs in GRCh38 and 313,838 mouse cCREs in mm10, with homologous cCREs cross-referenced across species
Search - ENCODE Homo sapiens activated T-helper 1 cell male adult (35 years) treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 30 ng mL Interleukin-12 subunit beta for 36 hours, 10 ng mL Interleukin-2 for 14 days, anti-CD3 and anti-CD28 coated beads for 14 days, 1 μg mL Interleukin-4 antibody for 36 hours, 30 ng mL Interleukin-12 subunit alpha for 36 hours
Access to ENCODE data The ENCODE portal contains these features to access, view, and download ENCODE data: Search metadata : The metadata describing the assays can be searched by entering any string into the text box in the upper right corner of the page or via the faceted browser