eyeIntegration_app: eyeIntegration Shiny App Code

Study Accession | Title | Tissue | DOI --- | --- | --- | ---- E_MTAB_4377 | An atlas of gene expression and gene co-regulation in the human retina | Retina | http://dx.doi.org/10.1093/nar/gkw486 SRP002881 | SplicePL: de novo splice junction detection from paired-end RNA-seq reads | Retina | - SRP011895 | Engineering a Blood‐Retinal Barrier With Human Embryonic Stem Cell‐Derived Retinal Pigment Epithelium: Transcriptome and Functional Analysis | RPE | http://dx.doi.org/10.5966/sctm.2012-0134 SRP012585 | Identification of miRNA signatures during the differentiation of hESCs into retinal pigment epithelial cells | ESC, RPE | http://dx.doi.org/10.1371/journal.pone.0037224 SRP012682 | Genotype-Tissue Expression (GTEx) Common Fund Project | Adipose Tissue, Adrenal Gland, Blood, Blood Vessel, Brain, Breast, Colon, Esophagus, Heart, Kidney, Liver, Lung, Muscle, Nerve, Pancreas, Pituitary, Salivary Gland, Skin, Small Intestine, Spleen, Stomach, Thyroid | http://dx.doi.org/10.1038/nature24277 SRP015336 | Unprecedented alternative splicing and 3 Mb of novel transcribed sequence leads to significant transcript diversity in the transcriptome of the human retina | Retina | http://dx.doi.org/10.1186/1471-2164-14-486 SRP016140 | Identification of Novel Molecular Markers through Transcriptomic Analysis in Human Fetal and Adult Corneal Endothelial Cells | Cornea | http://dx.doi.org/10.1093/hmg/dds527 SRP034875 | Comprehensive Analysis of Gene Expression in Human Retina and Supporting Tissues | Retina, RPE | http://dx.doi.org/10.1093/hmg/ddu114 SRP035641 | RNA-seq analysis in Cornea epithelial cells (CECs), skin epithelial cells (SECs), LSCs after knocking down PAX6 (3-D shPAX6 LSCs) and SESCs transduced with PAX6(3-D PAX6+ SESCs) upon 3-D differentiation | Cornea | http://dx.doi.org/10.1038/nature13465 SRP045639 | Aneuploidy-induced cellular stresses limit autophagic degradation. | RPE | http://dx.doi.org/10.1101/gad.269118.115 SRP053034 | The core spliceosome as target and effector of non-canonical ATM signalling | RPE | http://dx.doi.org/10.1038/nature14512 SRP055101 | Transcriptomic analysis of cultured corneal endothelial cells as a validation for their use in cell-replacement therapy | Cornea | http://dx.doi.org/10.3727/096368915X688948 SRP056957 | Transcriptome dynamics of developing photoreceptors in 3-D retina cultures recapitulates temporal sequence of human cone and rod differentiation revealing cell surface markers and gene networks | ESC, Retina | http://dx.doi.org/10.1002/stem.2122 SRP057295 | Restoration of mesenchymal retinal pigmented epithelial cells by TGFβ pathway inhibitors: implications for age-related macular degeneration | RPE | http://dx.doi.org/10.1186/s13073-015-0183-x SRP061670 | Homo sapiens Raw sequence reads | RPE | - SRP062870 | Deletion of DXZ4 on the human inactive X chromosome eliminates superdomains and impairs gene silencing | RPE | http://dx.doi.org/10.1073/pnas.1609643113 SRP064956 | An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes | RPE | http://dx.doi.org/10.1038/ncb3201 SRP079002 | Enriched retinal ganglion cells derived from human embryonic stem cells (RNA-seq) | ESC | http://dx.doi.org/10.1038/srep30552 SRP080002 | Transcriptome analysis reveals rod/cone photoreceptor specific signatures across mammalian retinas | Retina | http://dx.doi.org/10.1093/hmg/ddw268 SRP080886 | Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq | Retina, RPE | http://dx.doi.org/10.1016/j.exer.2014.11.001 SRP091605 | Transcriptomes during lens differentiation of human embryonic stem cells | ESC, Lens | - SRP050054 | Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets | Single Cell Mouse Retina | http://dx.doi.org/10.1016/j.cell.2015.05.002 SRP012585 | Identification of miRNA signatures during the differentiation of hESCs into retinal pigment epithelial cells | RPE | https://doi.org/10.1371/journal.pone.0037224 SRP018405 | High throughput gene expression analysis identifies reliable expression markers of human corneal endothelial cells. | Cornea | https://doi.org/10.1371/journal.pone.0067546 SRP035641 | RNA-seq analysis in Cornea epithelial cells (CECs), skin epithelial cells (SECs), LSCs after knocking down PAX6 (3-D shPAX6 LSCs) and SESCs transduced with PAX6(3-D PAX6+ SESCs) upon 3-D differentiation | Cornea | - SRP045639 | Aneuploidy-induced cellular stresses limit autophagic degradation | RPE | https://doi.org/10.1101/gad.269118.115 SRP091605 | Transcriptomes during lens differentiation of human embryonic stem cells | Lens | - SRP090226 | Long noncoding RNA related-competing endogenous RNAs in retinal pigment epithelial cells induced by clusterin | RPE | - SRP098761 | Comprehensive analysis of gene expression in human retina and supporting tissues | Retina, RPE | https://doi.org/10.1093/hmg/ddu114 SRP070938 | Restoration of Mesenchymal RPE by Transcription Factor-Mediated Reprogramming | RPE | https://doi.org/10.1167/iovs.16-20018 SRP094572 | Nicotinamide Ameliorates Disease Phenotypes in a Human iPSC Model of Age-related Macular Degeneration | RPE | https://doi.org/10.1016/j.stem.2016.12.015 SRP070148 | Collagen synthesis disruption and downregulation of core elements of TGF-β, Hippo, and Wnt pathways in keratoconus corneas | Cornea | https://doi.org/10.1038/ejhg.2017.4 SRP092413 | Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines | RPE | https://doi.org/10.1038/sdata.2017.33 SRP097696 | Identification of RUNX1 as a Mediator of Aberrant Retinal Angiogenesis | Retina Endothelium | https://doi.org/10.2337/db16-1035 SRP091675 | Appropriately differentiated ARPE-19 cells regain phenotype and gene expression profiles similar to those of native RPE cells | RPE | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5360456/ SRP090040 | The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis | Retina | https://doi.org/10.1016/j.neuron.2017.04.022 SRP075990 | Directed differentiation of human embryonic stem cells to corneal endothelial cell-like cells: A transcriptomic analysis | Cornea | https://doi.org/10.1016/j.exer.2016.08.004 SRP106457 | SAF-A Regulates Interphase Chromosome Structure through Oligomerization with Chromatin-Associated RNAs | RPE | https://dx.doi.org/10.1016%2Fj.cell.2017.05.029 SRP090027 | Homo sapiens Transcriptome or Gene expression | RPE | - SRP111145 | Retinal Pigment Epithelial Cells are a Potential Reservoir for Ebola Virus in the Human Eye | RPE | https://dx.doi.org/10.1167%2Ftvst.6.4.12 SRP093877 | Transcriptomic Profiling of Posterior Polymorphous Corneal Dystrophy | Cornea | https://doi.org/10.1167/iovs.17-21423 SRP108292 | Cellular responses to human cytomegalovirus infection: Induction of a mesenchymal-to-epithelial transition (MET) phenotype | RPE | https://doi.org/10.1073/pnas.1710799114 SRP110135 | Characterization of lincRNA expression in the human retinal pigment epithelium and differentiated induced pluripotent stem cells | RPE | https://doi.org/10.1371/journal.pone.0183939 SRP117613 | Treatment Paradigms for Retinal and Macular Diseases Using 3-D Retina Cultures Derived From Human Reporter Pluripotent Stem Cell Lines | Retina | https://doi.org/10.1167/iovs.15-17639 SRP119291 | Wnt5a Contributes to the Differentiation of Human Embryonic Stem Cells into Lentoid Bodies Through the Noncanonical Wnt/JNK Signaling Pathway | Lens | https://doi.org/10.1167/iovs.18-23902 SRP115908 | Spontaneous generation of a novel foetal human retinal pigment epithelium (RPE) cell line available for investigation on phagocytosis and morphogenesis | RPE | https://doi.org/10.1111/cpr.12386 ERP022243 | Giantin-knockout models reveal a feedback loop between Golgi function and glycosyltransferase expression | RPE | https://dx.doi.org/10.1242%2Fjcs.212308 SRP119766 | Molecular Anatomy of the Developing Human Retina | Retina | https://doi.org/10.1016/j.devcel.2017.10.029 SRP159246 | Thyroid hormone signaling specifies cone subtypes in human retinal organoids | Retina | https://doi.org/10.1126/science.aau6348