Abstract:The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome Project. The current database exceeds 6500 experiments across more than 450 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the H. sapiens and M. musculus genomes. All ENCODE experimental data, metadata, and associa… Show more
“…The design of the 4DN data portal infrastructure (Fig. 5 ), originally based on the ENCODE infrastructure, includes the following components: (1) A postgres database storing metadata in json format, first developed in ENCODE; (2) The python pyramid framework for the database known as SnoVault 52 , first developed in ENCODE but further tailored and developed by the 4DN DCIC ( https://github.com/4dn-dcic/snovault ); (3) The FourFront front-end ( https://github.com/4dn-dcic/fourfront ), originally based on EncodeD 52 from ENCODE, but engineered by 4DN DCIC to feature a data model for representing diverse datasets, and includes a modern front-end with reactJS to provide a responsive user experience; (4) Elasticsearch that provides fast and efficient search with various metadata fields by indexing all items and formatting them for retrieval; (5) AWS S3 used for file storage, enabling all public data files to be accessed via the data portal interface; (6) A RESTful API underlying the infrastructure, through which all metadata in the portal can be accessed. Fig.…”
The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in the nucleus and the impact of their disruption in disease biology. We present the 4DN Data Portal (https://data.4dnucleome.org/), a repository for datasets generated in the 4DN network and relevant external datasets. Datasets were generated with a wide range of experiments, including chromosome conformation capture assays such as Hi-C and other innovative sequencing and microscopy-based assays probing chromosome architecture. All together, the 4DN data portal hosts more than 1800 experiment sets and 36000 files. Results of sequencing-based assays from different laboratories are uniformly processed and quality-controlled. The portal interface allows easy browsing, filtering, and bulk downloads, and the integrated HiGlass genome browser allows interactive visualization and comparison of multiple datasets. The 4DN data portal represents a primary resource for chromosome contact and other nuclear architecture data for the scientific community.
“…The design of the 4DN data portal infrastructure (Fig. 5 ), originally based on the ENCODE infrastructure, includes the following components: (1) A postgres database storing metadata in json format, first developed in ENCODE; (2) The python pyramid framework for the database known as SnoVault 52 , first developed in ENCODE but further tailored and developed by the 4DN DCIC ( https://github.com/4dn-dcic/snovault ); (3) The FourFront front-end ( https://github.com/4dn-dcic/fourfront ), originally based on EncodeD 52 from ENCODE, but engineered by 4DN DCIC to feature a data model for representing diverse datasets, and includes a modern front-end with reactJS to provide a responsive user experience; (4) Elasticsearch that provides fast and efficient search with various metadata fields by indexing all items and formatting them for retrieval; (5) AWS S3 used for file storage, enabling all public data files to be accessed via the data portal interface; (6) A RESTful API underlying the infrastructure, through which all metadata in the portal can be accessed. Fig.…”
The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in the nucleus and the impact of their disruption in disease biology. We present the 4DN Data Portal (https://data.4dnucleome.org/), a repository for datasets generated in the 4DN network and relevant external datasets. Datasets were generated with a wide range of experiments, including chromosome conformation capture assays such as Hi-C and other innovative sequencing and microscopy-based assays probing chromosome architecture. All together, the 4DN data portal hosts more than 1800 experiment sets and 36000 files. Results of sequencing-based assays from different laboratories are uniformly processed and quality-controlled. The portal interface allows easy browsing, filtering, and bulk downloads, and the integrated HiGlass genome browser allows interactive visualization and comparison of multiple datasets. The 4DN data portal represents a primary resource for chromosome contact and other nuclear architecture data for the scientific community.
“…Each NGS run included 6 pooled libraries loaded into one NextSeq High Output cartridge (300 Cycles; Illumina). Paired-end sequencing was performed on a NextSeq 500 system (Illumina) with 152 cycles (76 bp PE sequencing) following Encode Project protocol for best RNA Seq data (12). Individual microdissected areas inside each sample are unique to that section and therefore not repeatable through biological replicates.…”
Laser capture microdissection (LCM) coupled with RNA-seq is a powerful tool to identify genes that are differentially expressed in specific histological tumor subtypes. To better understand the role of single tumor cell populations in the complex heterogeneity of glioblastoma, we paired microdissection and NGS technology to study intra-tumoral differences into specific histological regions and cells of human GBM FFPE tumors. We here isolated astrocytes, neurons and endothelial cells in 6 different histological contexts: tumor core astrocytes, pseudopalisading astrocytes, perineuronal astrocytes in satellitosis, neurons with satellitosis, tumor blood vessels, and normal blood vessels. A customized protocol was developed for RNA amplification, library construction, and whole transcriptome analysis of each single portion. We first validated our protocol comparing the obtained RNA expression pattern with the gene expression levels of RNA-seq raw data experiments from the BioProject NCBI database, using Spearman's correlation coefficients calculation. We found a good concordance for pseudopalisading and tumor core astrocytes compartments (0.5 Spearman correlation) and a high concordance for perineuronal astrocytes, neurons, normal, and tumor endothelial cells compartments (0.7 Spearman correlation). Then, Principal Component Analysis and differential expression analysis were employed to find differences between tumor compartments and control tissue and between same cell types into distinct tumor contexts. Data consistent with the literature emerged, in which multiple therapeutic targets significant for glioblastoma (such as Integrins, Extracellular Matrix, transmembrane transport, and metabolic processes) play a fundamental role in the disease progression. Moreover, specific cellular processes have been associated with certain cellular subtypes within the tumor. Our results are promising and suggest a compelling method for studying glioblastoma heterogeneity in FFPE samples and its application in both prospective and retrospective studies.
“…New data types, pipelines, metadata properties and ways of interacting with the data are continually being devised and improved upon. The Portal has seen many revisions since its launch in 2013 with new software releases occurring on average every three weeks ( 14 ). The release version can be found in the lower left corner of the Portal.…”
The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and metadata generated by the ENCODE Consortium. Two principles have motivated the design. First, experimental protocols, analytical procedures and the data themselves should be made publicly accessible through a coherent, web-based search and download interface. Second, the same interface should serve carefully curated metadata that record the provenance of the data and justify its interpretation in biological terms. Since its initial release in 2013 and in response to recommendations from consortium members and the wider community of scientists who use the Portal to access ENCODE data, the Portal has been regularly updated to better reflect these design principles. Here we report on these updates, including results from new experiments, uniformly-processed data from other projects, new visualization tools and more comprehensive metadata to describe experiments and analyses. Additionally, the Portal is now home to meta(data) from related projects including Genomics of Gene Regulation, Roadmap Epigenome Project, Model organism ENCODE (modENCODE) and modERN. The Portal now makes available over 13000 datasets and their accompanying metadata and can be accessed at: https://www.encodeproject.org/.
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