v9 Long Read RNASeq data from 88 GTEx tissue and cell line samples
CITATION: Glinos, D. A., Garborcauskas, G., Hoffman, P., Ehsan, N., Jiang, L., Gokden, A., ... & Cummings, B. B. (2022). Transcriptome variation in human tissues revealed by long-read sequencing. Nature, 608(7922), 353-359.
v8 Single-Tissue e/sQTL Data
CITATION: GTEx Consortium. (2020). The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science, 369(6509), 1318-1330.
GEO
URL: https://www.ncbi.nlm.nih.gov/geo/
DESCRIPTION: GEO is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles.
CITATION: Edgar, Ron, Michael Domrachev, and Alex E. Lash. "Gene Expression Omnibus: NCBI gene expression and hybridization array data repository." Nucleic acids research 30.1 (2002): 207-210.
Expression Atlas
URL:https://www.ebi.ac.uk/gxa/home
DESCRIPTION: Expression Atlas is an open science resource that gives users a powerful way to find information about gene and protein expression. Our mission is to provide the scientific community with freely available information on the abundance and localisation of RNA (and proteins) across species and biological conditions such as different tissues, cell types, developmental stages and diseases among others.
CITATION: Papatheodorou, Irene, et al. "Expression Atlas update: from tissues to single cells." Nucleic acids research 48.D1 (2020): D77-D83.
TCGA
FULL NAME:The Cancer Genome Atlas
URL: https://portal.gdc.cancer.gov/
CITATION:
-Tomczak, Katarzyna, Patrycja Czerwińska, and Maciej Wiznerowicz. "Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge." Contemporary Oncology/Współczesna Onkologia 2015.1 (2015): 68-77.
The Cancer Genome Atlas Research Network., Weinstein, J., Collisson, E. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 45, 1113–1120 (2013). https://doi.org/10.1038/ng.2764
GENT2
URL: http://gent2.appex.kr/gent2/
DESCRIPTION: Gene Expression database of Normal and Tumor tissues 2 (GENT2)
CITATION: Park, Seung-Jin, et al. "GENT2: an updated gene expression database for normal and tumor tissues." BMC medical genomics 12.5 (2019): 1-8.
GEN
FULL NAME: Gene Expression Nebulas
URL: https://ngdc.cncb.ac.cn/gen/
DESCRIPTION: Gene Expression Nebulas (GEN) is a data portal of transcriptomic profiles under various conditions derived entirely from bulk and single-cell RNA-Seq data analysis in multiple species.
CITATION:Zhang, Yuansheng, et al. "Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels." Nucleic Acids Research 50.D1 (2022): D1016-D1024.
The Human PRotein Atlas
URL : https://www.proteinatlas.org/
DESCRIPTION: The Human Protein Atlas is a Swedish-based program initiated in 2003 with the aim to map all the human proteins in cells, tissues, and organs using an integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.
CITATION: Uhlén, Mathias, et al. "Proteomics. Tissue-based map of the human proteome." Science (New York, NY) 347.6220 (2015): 1260419-1260419.
HTCA
FULL NAME: The Human Transcriptome Cell Atlas
URL: https://www.htcatlas.org/
DESCRIPTION: A comprehensive assessment of human transcriptomes at single-cell level.