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714 results for “Functional Genomics”
Genome, repeat, and functional annotation associated with the naked mole-rat genome assembly, mHetGlaV3 (GCA_964261345.1)
<p>The naked mole-rat (NMR; Heterocephalus glaber) is a eusocial subterranean rodent with a highly unusual set of physiological traits, such as extreme longevity, that has attracted great interest amongst the scientific community. However, the genetic basis of most of these traits has not been elucidated. To facilitate our understanding of the molecular mechanisms underlying NMR physiology and behaviour, we generated a long-read chromosomal-level genome assembly of the NMR. This genome, mHetGlaV2, was subsequently annotated and incorporated into a “91 eutherian mammals” multiple whole genome alignment in Ensembl. </p> <p>We identified intra-chromosomal misassemblies within mHetGlaV2. We fixed these misassemblies by comparing syntenic blocks between this assembly and the Canadian Porcupine (EreDor) genome assembly (https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_028451465.1/) and a FISH-Karyotype of the naked mole-rat completed by Romanenko et al., 2023 (PMID: 380307020) to address any misassemblies and place centromeres. Chromosome numbering was identified from a composite karyogram of karyotypes from over 350 cells. This scaffold-corrected assembly is labelled mHetGlaV3 (https://www.ebi.ac.uk/ena/browser/view/GCA_964261345.1).</p> <p>This repository stores the repeat, genome, and epigenome annotations for HetGlaV3.</p> <p>mHetGlaV3.primary.gtf.gz. Gene structures and gene symbols are transferred from ENSEMBL annotations of mHetGlaV2 using liftOff with default parameters. Additional gene symbols were identified using TOGA and manual curation.</p> <p>mHetGlaV3.primary.gtf.gz. Simple repetitive regions and transposable elements were annotated using EarlGrey (https://github.com/TobyBaril/EarlGrey) using "Rodentia" annotations for RepeatMasker.</p> <p>mHetGlaV3.primary.genesymbol_table.txt.txt.gz. A tab-delimited file where rows are gene IDs and columns are gene symbols generated with each method. "Consensus" shows the best matching gene symbol for each gene ID.</p> <p>mHetGlaV3.primary_annotated_blacklist.bed.gz. Provides an assembly "blacklist" for mHetGlaV3. This blacklist is a bed file annotating assembly breakpoints between HetGlaV2 and HetGlaV3. This blacklist contains additional columns (e.g., closest gene, overlapping TE etc.) and should therefore be filtered to the first column before being incorporated into traditional genomic pipelines.</p> <p>mHetGlaV3.primary_hypothalamus_ABC_enhancer.bedpe.gz. Activity-By-Contact enhancers (https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction) generated in the female subordinate naked mole-rat hypothalamus using Hi-C-seq, ChIP-seq of H3K27Ac data, ATAC-seq, and RNA-seq information.</p> <p>mHetGlaV3.primary_hypothalamus_chromHMM.bed.gz. Chromatin states (using Chromhmm) annotating the female subordinate naked mole-rat hypothalamus using H3K4me3 (promoter), H4K4me2 (promoter-enhancer), H3K27Ac (active enhancer), H3K36me3 (elongated), H3K27me3 (polycomb repressed), H3K9me3 (heterochromatin), and CTCF (whole brain) ChIP-seq data, as well as ATAC-seq and RNA-seq data.</p> <p>mHetGlaV3.primary.fa.gz. Genome assembly fasta file for the naked mole-rat (V3, primary assembly). This assembly matches the primary assembly stored on ENA, however the chromosome names match these files, rather than have chromosome names processed by ENA (e.g. chr 1 instead of "OZ179169.1 Heterocephalus glaber genome assembly, chromosome: 1").</p> <p> </p> <p>UPDATES:</p> <p>* The 1.2 update fixed unscaffolded contig names from those used in-lab to those compatible with ENA.</p> <p>* The 1.3 update added small (50~100kbp) contigs onto mHetGlaV3.primary.fa.gz that were filtered before the ENA submission.</p> <p>* The 1.4 update fixed a small chromosome naming inconsistency spotted in the 1.3 update.</p>
Summary statistics accompanying the article "Genome-wide association study of the human brain functional connectome reveals strong vascular component underlying global network efficiency" in Scientific Reports (2022)
<p>Summary statistics for genome-wide association studies reported in:</p> <p>Bell, S., Tozer, D.J., & Markus H.S. (2022). Genome-wide association study of the human brain functional connectome reveals strong vascular component underlying global network efficiency. <em>Scientific Reports</em>, DOI: <a href="https://dx.doi.org/10.1038/s41598-022-19106-7">10.1038/s41598-022-19106-7</a>. </p> <p><strong>Abstract</strong></p> <p>Complex brain networks play a central role in integrating activity across the human brain, and such networks can be identified in the absence of any external stimulus. We performed 10 genome-wide association studies of resting state network measures of intrinsic brain activity in up to 36,150 participants of European ancestry in the UK Biobank. We found that the heritability of global network efficiency was largely explained by blood oxygen level-dependent (BOLD) resting state fluctuation amplitudes (RSFA), which are thought to reflect the vascular component of the BOLD signal. RSFA itself had a significant genetic component and we identified 24 genomic loci associated with RSFA, 157 genes whose predicted expression correlated with it, and 3 proteins in the dorsolateral prefrontal cortex and 4 in plasma. We observed correlations with cardiovascular traits, and single-cell RNA specificity analyses revealed enrichment of vascular related cells. Our analyses also revealed a potential role of lipid transport, store-operated calcium channel activity, and inositol 1,4,5-trisphosphate binding in resting-state BOLD fluctuations. We conclude that that the heritability of global network efficiency is largely explained by the vascular component of the BOLD response as ascertained by RSFA, which itself has a significant genetic component.</p> <p> </p> <p>Further information on the files uploaded here can be found in the README. Users interested in bulk downloading these summary statistics may find <a href="https://github.com/dvolgyes/zenodo_get">zenodo_get</a> helpful.</p>
Genome-wide structure and function modeling of SARS-COV-2
<p>Homology models and function annotation for all proteins in the SARS-CoV-2 genome. For a description of each file, follow <a href="https://zhanglab.ccmb.med.umich.edu/COVID-19/">this link</a>. </p>
Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa.
<p>BACKGROUND:</p> <p>Turkey is a crossroads of major population movements throughout history and has been a hotspot of cultural interactions. Several studies have investigated the complex population history of Turkey through a limited set of genetic markers. However, to date, there have been no studies to assess the genetic variation at the whole genome level using whole genome sequencing. Here, we present whole genome sequences of 16 Turkish individuals resequenced at high coverage (32×-48×).</p> <p>RESULTS:</p> <p>We show that the genetic variation of the contemporary Turkish population clusters with South European populations, as expected, but also shows signatures of relatively recent contribution from ancestral East Asian populations. In addition, we document a significant enrichment of non-synonymous private alleles, consistent with recent observations in European populations. A number of variants associated with skin color and total cholesterol levels show frequency differentiation between the Turkish populations and European populations. Furthermore, we have analyzed the 17q21.31 inversion polymorphism region (MAPT locus) and found increased allele frequency of 31.25% for H1/H2 inversion polymorphism when compared to European populations that show about 25% of allele frequency.</p> <p>CONCLUSION:</p> <p>This study provides the first map of common genetic variation from 16 western Asian individuals and thus helps fill an important geographical gap in analyzing natural human variation and human migration. Our data will help develop population-specific experimental designs for studies investigating disease associations and demographic history in Turkey.</p>
Functional genomics analysis to disentangle the role of genetic variants in major depression - Supplementary Tables
<p>This entry contains the data generated by the study "Functional genomics analysis to disentangle the role of genetic variants in major depression" that are part of the Supplementary information of the article describing the study.</p> <p>The entry contains the following data:</p> <p><strong>Supplementary Tables S1-S7</strong></p> <p>Supplementary Table S1. Summary of resources.</p> <p>Supplementary Table S2. Causal GVs for MD.</p> <p>Supplementary Table S3. pGenes functional and disease enrichment analysis.</p> <p>Supplementary Table S4. Fine-mapped MD causal GVs disease enrichment analysis.</p> <p>Supplementary Table S5. Colocalizing GWAS-eQTLs association to disease.</p> <p>Supplementary Table S6. TFBS analysis.</p> <p>Supplementary Table S7. GVs state annotation. </p>
Joint AstraZeneca-Cancer Research Horizons Functional Genomics Centre's CRISPRn library benchmark screens: gRNA counts and associated metadata
<p>Genome-wide CRISPR sgRNA libraries have emerged as transformative tools to systematically probe gene function. While these libraries have been iterated over time to be more efficient, their large size limits their use in some applications. Here, we benchmarked publicly available genome-wide single-targeting sgRNA libraries and evaluated dual targeting as a strategy for pooled CRISPR loss-of-function screens. We leveraged this data to design two minimal genome-wide human CRISPR-Cas9 libraries that are 50% smaller than other libraries and that preserve specificity and sensitivity, thus enabling broader deployment at scale. </p>
RNA-seq dataset for Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism
<p>Data to be used along with <a href="https://github.com/neelroop/asd-development-coexpression-2013">code</a> from 2013 paper that was originally on a site hosted at UCLA, but may no longer be accessible.</p>
Functional genomics and co-occurrence in a diverse tropical tree genus: The roles of drought and defense related genes
<p>Tropical tree communities are among the most diverse in the world. A small number of genera often disproportionately contribute to this diversity. How so many species from a single genus can co-occur represents a major outstanding question in biology. Niche differences are likely to play a major role in promoting congeneric diversity, but the mechanisms of interest are often not well-characterized by the set of functional traits generally measured by ecologists. To address this knowledge gap, we used a functional genomic approach to investigate the mechanisms of co-occurrence in the hyper-diverse genus <em>Ficus</em>. Our study focused on over 800 genes related to drought and defense, providing detailed information on how these genes may contribute to the diversity of <em>Ficus</em> species. We find widespread and consistent evidence of the importance of defense gene dissimilarity in co-occurring species, providing genetic support for what would be expected under the Janzen-Connell mechanism. We also find that drought-related gene sequence similarity is related to <em>Ficus</em> co-occurrence, indicating that similar responses to drought promote co-occurrence. We provide the first detailed functional genomic evidence of how drought- and defense-related genes simultaneously contribute to the local co-occurrence in a hyper-diverse genus. Our results demonstrate the potential of community transcriptomics to identify the drivers of species co-occurrence in hyper-diverse tropical tree genera.</p>
Global Functional Genomics Reveals GRK5 as a Therapeutic Target for Cystic Fibrosis
<p>Cystic Fibrosis (CF) is a life-shortening disease affecting >90,000 individuals worldwide predominantly with respiratory symptoms. About 80% of individuals with CF have the F508del mutation that causes the CF transmembrane conductance regulator (CFTR) protein to misfold and be targeted for premature degradation by the endoplasmic reticulum (ER) quality control (ERQC), thus preventing its plasma membrane (PM) traffic. Despite the recent approval of a ‘highly effective’ drug rescuing F508del-CFTR, maximal lung function improvement is ~14% and the drug-targeted genes remain unknown.</p> <p>To identify global modulators of F508del traffic, we performed a high-content siRNA microscopy-based screen of >9,000 genes and monitored F508del-CFTR PM rescue in human airway cells. This primary screen identified 227 F508del-CFTR traffic regulators, of which 35 could be validated by additional siRNAs. Subsequent mechanistic studies established GRK5 as a robust regulator whose inhibition rescues F508del-CFTR PM traffic, thus emerging as a novel potential drug target for CF.</p>
Functional and molecular characterization of suicidality factors using phenotypic and genome-wide data
<p>GWAS summary statistics for Functional and molecular characterization of suicidality factors using phenotypic and genome-wide data published in Molecular Psychiatry by Quintero Reis A, Newton BA, Kessler R, Polimanti R, and Wendt FR.</p>
Genome sequencing of 2,000 canids advances the understanding of demography, genome function and architecture
<p><strong>Background: </strong>The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20x data from 1,987 individuals, including 1,611 dogs (321 breeds), 309 village dogs, 63 wolves and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility and genome architecture and function.</p> <p><strong>Results: </strong>We report the analysis of >48M single nucleotide, indel, and structural variants spanning the autosomes, X chromosome and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.</p> <p><strong>Conclusions:</strong> We have developed a dense dataset of 1,987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available</p>
Functional genomics and co-occurrence in a diverse tropical tree genus: The roles of drought and defense related genes
Open the record for dataset details and reuse information.
Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome - datasets
<p>This is an archive of the repository held under https://github.com/dmnfarrell/gordon-group/tree/master/mbovis_annotation</p> <p>It contains a notebook and required input files for updating the MTB/Mbovis AF2122/97 genomes with new protein product annotations from literature.</p> <p>D Farrell UCD February 2020</p> <p>Updates to M.bovis genome (Aug 2019):<br> added 611 product annotations<br> added 689 gene names<br> added 5 manually edited entries from pdb hits<br> removed locus_tags for repeat_region features<br> added prefix to tRNA and mobile_element features for consistency</p> <p><br> References<br> Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome (https://www.biorxiv.org/content/10.1101/757823v1)</p>
Data from: Integrative genomic analysis in African American children with asthma finds 3 novel loci associated with lung function
<p>Bronchodilator drugs are commonly prescribed for treatment and management of obstructive lung function present with diseases such as asthma. Administration of bronchodilator medication can partially or fully restore lung function as measured by pulmonary function tests. The genetics of baseline lung function measures taken prior to bronchodilator medication has been extensively studied, and the genetics of the bronchodilator response itself has received some attention. However, few studies have focused on the genetics of post-bronchodilator lung function. To address this gap, we analyzed lung function phenotypes in 1,103 subjects from the Study of African Americans, Asthma, Genes, and Environment (SAGE), a pediatric asthma case-control cohort, using an integrative genomic analysis approach that combined genotype, locus-specific genetic ancestry, and functional annotation information. We integrated genome-wide association study (GWAS) results with an admixture mapping scan of three pulmonary function tests (FEV1, FVC, and FEV1/FVC) taken before and after albuterol bronchodilator administration on the same subjects, yielding six traits. We identified 18 GWAS loci, and 5 additional loci from admixture mapping, spanning several known and novel lung function candidate genes. Most loci identified via admixture mapping exhibited wide variation in minor allele frequency across genotyped global populations. Functional fine-mapping revealed an enrichment of epigenetic annotations from peripheral blood mononuclear cells, fetal lung tissue, and lung fibroblasts. Our results point to three novel potential genetic drivers of pre- and post-bronchodilator lung function: ADAMTS1, RAD54B, and EGLN3. </p>
Data from: Genome duplication effects on functional traits and fitness are genetic context and species dependent: studies of synthetic polyploid Fragaria
PREMISE OF THE STUDY Divergence in functional traits and adaptive responses to environmental change underlies the ecological advantage of polyploid plants in the wild. While established polyploids may benefit from combined outcomes of genome doubling, hybridization and polyploidy-enabled adaptive evolution, it remains less clear whether genome doubling alone can drive ecological divergence or whether the outcome is genetically variable.METHODS Using synthetic, colchicine-induced, autotetraploid (4x) plants derived from self-pollinated diploid (2x) seeds, and their colchicine-treated but unconverted diploid (2x.nc) full sibs from two diploid wild strawberry taxa (Fragaria vesca ssp. vesca and F. vesca ssp. bracteata), we examined the effects of genome doubling on functional traits, heat stress tolerance and fitness components across taxa and maternal families (i.e. genetic families) within taxa.KEY RESULTS Comparisons between 2x and 2x.nc plants indicated a negligible effect of colchicine treatment on functional traits. Genome doubling increased stomatal length, and decreased stomatal density, specific leaf area and leaf vein density, recapitulating patterns observed in wild polyploid Fragaria. Trichome density, heat stress tolerance and relative growth rate were not significantly affected by genome doubling. Although a reduction in clonal reproduction was observed in response to genome doubling, this effect was strongly genetic family dependent.CONCLUSIONS The results suggest that genome doubling during incipient speciation alone can generate ecological divergence and variation among genetic lineages. This response potentially allows for rapid short-term evolutionary adaptation and fuels genomic diversity and independent origins of polyploidy.
Identification and analysis of functional associations among natural eukaryotic genome editing components
<p>The contents of the data files for the manuscript "Identification and analysis of functional associations among natural eukaryotic genome editing components" are described below.</p> <p>Dataset 1 - ies_retention.tab<br> = All IES retention scores used in the manuscript</p> <p>Dataset 2 - oes_retention.tab<br> = OES retention estimates.</p> <p>Supplementary Data S1 - ies_retention_score_correlation_stats_all.txt<br> = Statistics for Spearman's correlations for all IESs.</p> <p>Supplementary Data S2 - ies_retention_score_correlation_stats_len_le_35bp.txt<br> = Statistics for Spearman's correlations for IESs <= 35 bp.</p> <p>Supplementary Data S3 - ies_retention_score_correlation_stats_len_ge_500bp.txt<br> = Statistics for Spearman's correlations for IESs >= 500 bp.</p> <p>Supplementary Data S4 - oes_retention_score_correlation_stats_all.txt<br> = Statistics for Spearman's correlations for OESs (>= 300 bp and 3x-70x PGM-KD<br> coverage).</p> <p>Supplementary Data S5 - ies_retention_score_correlation.comparison_stats.txt<br> = Statistics for comparisons of Spearman correlation differences for all IESs.</p> <p>Supplementary Data S6 - oes_retention_score_correlation.comparison_stats.txt<br> = Statistics for comparisons of Spearman correlation differences for all OESs.</p> <p>Supplementary Data S7 - ies_vs_oes_retention_score_correlation.comparisons_stats.txt<br> = Statistics for comparisons of the differences in Spearman correlations<br> between IESs and OESs.</p> <p>Supplementary Data S8 - OES.v1.fa<br> = OES sequences.</p> <p> </p>
DeepAnnotation: A novel interpretable deep learning-based genomic selection model that integrates comprehensive functional annotations
<p>1. Update package, example dataset, and demo code of DeepAnnotation</p> <p>2. Update the transformed genotype data, the phenotype data, the comprehensive functional annotation data for Duroc prepared by RNAfold, DeepSEA, easyMF models, and the four types of input data for training DeepAnnotation model</p> <p>3. Add the conserved functional annotation</p> <p> </p>
Genome Database: Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers
<p>This repository contains the dataset used in the publication "Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers," which is currently under revision. A pre-print can be found <a href="https://doi.org/10.1101/2022.12.29.522137">here</a>. The database is based on previously published work to create a genomic database of honeybee gut microbes by Kirsten Ellegaard (2021), found <a href="https://zenodo.org/records/4661061">here.</a></p><p>The zipped folder deposited here after unzipping, should contain the following files and directories:</p><ul><li>honeybee_genome.fasta : fasta file containing the host (<i>Apis mellifera</i>) genome sequence</li><li>beebiome_db : fasta file of 198 concatenated genomes with one genome per entry (multi-line fasta) where the headers represent the genome identifier</li><li>beebiome_red_db : fasta file of 39 species representative genomes with one genome per entry (multi-line fasta) where the headers represent the genome identifier to be used for the analysis of intra-specific variation</li><li>fna_files : directory containing genome sequence files and concatenated files where the concatenated files contain one fasta entry renamed to the genome identifier and all contigs concatenated into one entry</li><li>ffn_files : directory containing one file per genome listing the nucleotide sequence of all the predicted genes</li><li>faa_files : directory containing one file per genome listing the amino acid sequence of all the predicted genes</li><li>bed_files : directory containing bed files where the location of each of the predicted genes are indicated based on their position in the concatenated genome file</li><li>single_ortho : directory containing one file per phylotype listing all the single-copy orthogroups (OGs) identified by orthofinder where each line represents an OG id followed by a list of genes from each of the genomes of that phylotype that belong to that OG and the corresponding sequences of these genes can be found in the ffn file belonging to the respective genome</li><li>red_bed_files : directory containing bed files for species representative genomes that only list the positions genes that belong to the core orthogroups of their phylotype</li></ul><p>Further information about how this genome database was used to analyze strain-level diversity can be found in the publication and accompanying code repository.</p>
Microsatellite exploration in the climbing hydrangea (Hydrangea petiolaris Siebold & Zucc.) transcriptome: A resource for population genetics and functional genomics
<p><strong>Background</strong></p> <p><em>Hydrangea petiolaris</em> Siebold & Zucc., also known as climbing hydrangea, is a vine native to the woodlands of Korea, Japan, and Sakhalin Island. It is an economically important ornamental plant with fertile and sterile flowers. Despite the recent increase in <em>Hydrangea</em> breeding and interest in germplasm conservation, relatively little is known about the relationships between <em>Hydrangea</em> species.</p> <p><strong>Results</strong></p> <p>We employed Illumina NovaSeq 6000 sequencing technology to generate a total of 39,945,480 reads, which were assembled into 137,715 contigs. A total of 109,092 filtered transcripts were used to identify microsatellites, and 54,587 microsatellite repeat motifs were revealed within 33,556 contigs. Among these, 4,510 transcripts harboring microsatellites had Gene Ontology annotations, and numerous microsatellite-containing transcripts exhibited associations with genes, including those encoding PPR proteins, aldehyde dehydrogenases, and bHLH transcription factors, related to the <em>restorer of fertility</em> (<em>Rf</em>) genes, which play a critical role in restoring fertility in plants with cytoplasmic male sterility. Validation of transcriptomic SSR markers demonstrated high levels of polymorphism, revealing significant genetic diversity within populations. However, null alleles and deviations from Hardy‒Weinberg equilibrium at specific loci suggested caution in genotyping accuracy. Population-level analysis disclosed high genetic differentiation and distinct clustering of populations.</p> <p><strong>Conclusions</strong></p> <p>The <em>H</em>. <em>petiolaris</em> transcriptomic SSR markers offer valuable insight for gaining insights into the population genetics, evolutionary background, and practical strategies for conserving this species. Moreover, the microsatellite loci we have identified and their associations with annotated genes hold promise for creating functional markers specifically tailored for <em>H</em>. <em>petiolaris</em>. These markers include valuable resources of transcriptomic SSR markers suitable for population genetic investigations and have a reasonable degree of applicability across different taxa.</p>
"Global Functional Genomics Reveals GRK5 as a Therapeutic Target for Cystic Fibrosis", CFTR interactomes
<p><em>A tidy selection of published CFTR interactomes (or CFTR-related omics datasets)</em></p> <p>Collects data from the original online sources, converts gene/protein identifiers into a standard tidy format and updates the identifiers. The Uniprot ID is taken as reference and all other identifiers are genereated from them. This causes some datasets to end up with less genes/proteins than reported.</p> <p>Datasets included</p> <ul> <li><strong>Botelho (2021)</strong> - CFTR traffic regulators <ul> <li>Botelho <em>et al</em> (2022), submitted</li> </ul> </li> <li><strong>Pankow (2015)</strong> - CFTR interactome <ul> <li>Pankow <em>et al</em> (2015) deltaF508 CFTR interactome remodelling promotes rescue of cystic fibrosis. <em>Nature</em>. 528, 510--516. <a href="https://doi.org/10.1038/nature15729">https://doi.org/10.1038/nature15729</a></li> </ul> </li> <li><strong>Canato (2018)</strong> - CFTR interactome <ul> <li>Canato <em>et al</em> (2018) Proteomic interaction profiling reveals KIFC1 as a factor involved in early targeting of F508del-CFTR to degradation. <em>Cell Mol Life Sci</em>. 75(24):4495-4509. <a href="https://doi.org/10.1007/s00018-018-2896-7">https://doi.org/10.1007/s00018-018-2896-7</a></li> </ul> </li> <li><strong>Santos (2019)</strong> - CFTR interactome <ul> <li>Santos <em>et al</em> (2019) Folding Status Is Determinant over Traffic-Competence in Defining CFTR Interactors in the Endoplasmic Reticulum. <em>Cells</em>. 8(4):353. <a href="https://doi.org/10.3390/cells8040353">https://doi.org/10.3390/cells8040353</a></li> </ul> </li> <li><strong>Hutt (2018)</strong> - CFTR interactome <ul> <li>Hutt <em>et al</em> (2018) A Proteomic Variant Approach (ProVarA) for Personalized Medicine of Inherited and Somatic Disease. <em>J Mol Biol</em>. 430: 2951-2973. <a href="https://doi.org/10.1016/j.jmb.2018.06.017">https://doi.org/10.1016/j.jmb.2018.06.017</a></li> </ul> </li> <li><strong>Rauniyar (2014)</strong> - CFTR proteome <ul> <li>Rauniyar <em>et al</em> (2014) Quantitative Proteomic Profiling Reveals Differentially Regulated Proteins in Cystic Fibrosis Cells. <em>J Proteome Res</em>. 13(11): 4668-4675. <a href="https://doi.org/10.1021/pr500370g">https://doi.org/10.1021/pr500370g</a></li> </ul> </li> <li><strong>Almaça (2013)</strong> - ENaC regulome <ul> <li>Almaça <em>et al</em> (2013) High-content siRNA screen reveals global ENaC regulators and potential cystic fibrosis therapy targets. <em>Cell</em>. 154(6):1390-400. <a href="https://doi.org/10.1016/j.cell.2013.08.045">https://doi.org/10.1016/j.cell.2013.08.045</a></li> </ul> </li> <li><strong>Tomati (2018)</strong> - CFTR regulome <ul> <li>Tomati <em>et al</em> (2018) High-throughput screening identifies FAU protein as a regulator of mutant cystic fibrosis transmembrane conductance regulator channel. <em>J Biol Chem</em>. 293(4):1203-1217. <a href="https://doi.org/10.1074/jbc.m117.816595">https://doi.org/10.1074/jbc.m117.816595</a></li> </ul> </li> <li><strong>Simpson (2012)</strong> - Secretome <ul> <li>Simpson <em>et al</em> (2012) Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway. <em>Nature Cell Biology</em>. 14, 764-774. <a href="https://doi.org/10.1038/ncb2510">https://doi.org/10.1038/ncb2510</a></li> </ul> </li> <li><strong>Wang (2006)</strong> - CFTR interactome <ul> <li>Wang <em>et al</em> (2006) Hsp90 Cochaperone Aha1 Downregulation Rescues Misfolding of CFTR in Cystic Fibrosis. <em>Cell</em>. 127(4):803-815. <a href="https://doi.org/10.1016/j.cell.2006.09.043">https://doi.org/10.1016/j.cell.2006.09.043</a></li> </ul> </li> <li><strong>Reilly (2017)</strong> - CFTR interactome <ul> <li>Reilly <em>et al</em> (2017) Targeting the PI3K/Akt/mTOR signalling pathway in Cystic Fibrosis. <em>Sci Rep</em>. 9;7(1):7642. <a href="https://doi.org/10.1038/s41598-017-06588-z">https://doi.org/10.1038/s41598-017-06588-z</a></li> </ul> </li> <li><strong>Gilchrist (2006)</strong> - Secretome <ul> <li>Gilchrist <em>et al</em> (2006) Quantitative Proteomics Analysis of the Secretory Pathway. <em>Cell</em>. 127(6):1265-1281. <a href="https://doi.org/10.1016/j.cell.2006.10.036">https://doi.org/10.1016/j.cell.2006.10.036</a></li> </ul> </li> <li><strong>Pankow (2019)</strong> - CFTR interactome <ul> <li>Pankow <em>et al</em> (2019) A posttranslational modification code for CFTR maturation is altered in cystic fibrosis. <em>Science Signaling</em>. 12(562):eaan7984. <a href="https://doi.org/10.1126/scisignal.aan7984">https://doi.org/10.1126/scisignal.aan7984</a></li> </ul> </li> <li><strong>Dang (2020)</strong> - CF lung disease modifier genes <ul> <li>Dang <em>et al</em> (2020) Mining GWAS and eQTL data for CF lung disease modifiers by gene expression imputation. <em>PLoS One</em>. 15(11):e0239189. <a href="https://doi.org/10.1371/journal.pone.0239189">https://doi.org/10.1371/journal.pone.0239189</a></li> </ul> </li> <li><strong>Hodos (2020)</strong> - CF genomic meta-analysis <ul> <li>Hodos <em>et al</em> (2020) Integrative genomic meta-analysis reveals novel molecular insights into cystic fibrosis and deltaF508-CFTR rescue. <em>Sci Rep</em> 10(1):20553. <a href="http://dx.doi.org/10.1038/s41598-020-76347-0">http://dx.doi.org/10.1038/s41598-020-76347-0</a></li> </ul> </li> </ul>
ScienceDex guides
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.