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Commit 6f975956 authored by Albert Hornos Vidal's avatar Albert Hornos Vidal
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feat: show host sequences studies data

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data/c19dpes_genomics_host_sequences.json 0 → 100644
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{"entity":"EGA COVID19 spanish PI studies","timestamp":"2021-10-14 08:46:48.293964","links":{"self":{"href":"https:\/\/docs.google.com\/spreadsheets\/d\/e\/2PACX-1vRgouM0eO0qKvyi43S72V-x3U80vru5dOkvL9jI9lO0wYeY6A11TK5UPWlcYCCevlm7isZLzaiLfsIW\/pub?gid=304192027&single=true&output=tsv"},"origin":{"href":"https:\/\/docs.google.com\/spreadsheets\/d\/e\/2PACX-1vRgouM0eO0qKvyi43S72V-x3U80vru5dOkvL9jI9lO0wYeY6A11TK5UPWlcYCCevlm7isZLzaiLfsIW\/pub?gid=304192027&single=true&output=tsv"}},"ega_studies_counter":23,"ega_datasets_counter":65,"ega_studies":[{"study_accession":"EGAS00001005465","study_title":"Multi-omic single-cell profiling of peripheral blood immune cells from COVID-19 patients and controls.","datasets":[{"dataset_accession":"EGAD00001007867","dataset_title":"Cambridge COVID-19 Single-cell PBMC"},{"dataset_accession":"EGAD00001007866","dataset_title":"Newcastle COVID-19 Single-cell PBMC"},{"dataset_accession":"EGAD00001007865","dataset_title":"UCL COVID-19 Single-cell PBMC"}]},{"study_accession":"EGAS00001005332","study_title":"COVID-19 whole blood transcriptomic analysis","datasets":[{"dataset_accession":"EGAD00001007776","dataset_title":"Whole blood RNA-sequencing of covid-19 patients and healthy controls"}]},{"study_accession":"EGAS00001005380","study_title":"An analysis of humoral and cellular immune responses following COVID-19 vaccination.","datasets":[{"dataset_accession":"EGAD00001007777","dataset_title":"Covid vaccination BCR repertoire analysis"}]},{"study_accession":"EGAS00001004571","study_title":"ScRNA-seq of PBMC and whole blood samples reveals a dysregulated myeloid cell compartment in severe COVID-19","datasets":[{"dataset_accession":"EGAD00001006550","dataset_title":"ScRNA-seq of PBMC and whole blood samples reveales a dysregulated myeloid cell compartment in severe COVID-19"}]},{"study_accession":"EGAS00001005060","study_title":"SARS-CoV-2 escapes CD8 T cell surveillance via mutations in MHC-I restricted epitopes [10x]","datasets":[{"dataset_accession":"EGAD00001008109","dataset_title":"analysis of T cell receptor repertoirs"},{"dataset_accession":"EGAD00001006995","dataset_title":"Single-cell gene expression data from CD8+ T cells from two Austrian COVID19 patients stimulated with wildtype and mutant SARS-Cov-2 peptides"}]},{"study_accession":"EGAS00001004508","study_title":"Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2","datasets":[{"dataset_accession":"EGAD00001006242","dataset_title":"Single cell RNA sequencing data in \"Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2\""},{"dataset_accession":"EGAD00001006241","dataset_title":"Bulk RNA sequencing data in \"Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2\""}]},{"study_accession":"EGAS00001004951","study_title":"Upper respiratory microbiome of COVID-19 patients","datasets":[{"dataset_accession":"EGAD00001006864","dataset_title":"CONTAGIOUS trial - COVID-19 16S dataset"},{"dataset_accession":"EGAD00001008006","dataset_title":"CONTAGIOUS trial - COVID-19 16S metadata"}]},{"study_accession":"EGAS00001004502","study_title":"Swarm Learning to identify COVID-19 tuberculosis and leukemia patients based on blood transcriptomes","datasets":[{"dataset_accession":"EGAD00001006231","dataset_title":"Swarm Learning to identify COVID-19 tuberculosis and leukemia patients based on blood transcriptomes "}]},{"study_accession":"EGAS00001005280","study_title":"Impaired Humoral and Cellular Immunity after SARS-CoV2 BNT162b2 (Tozinameran) Prime-Boost Vaccination in Kidney Transplant Recipients","datasets":[{"dataset_accession":"EGAD00001007689","dataset_title":"RNA-Seq of response to Tozinameran vaccination in individuals with KTx\/dialysis or healthy controls."}]},{"study_accession":"EGAS00001004689","study_title":"COVID-19 Postmortem Lung snRNA-seq","datasets":[{"dataset_accession":"EGAD00001006584","dataset_title":"COVID-19 Postmortem Lung snRNA-seq"}]},{"study_accession":"EGAS00001005039","study_title":"SINGLE-CELL RNA SEQUENCING Single-cell RNA sequencing was performed on 13 \u2018mild-moderate\u2019 and 10 \u2018critical\u2019 COVID19 PBMC samples","datasets":[{"dataset_accession":"EGAD00001006997","dataset_title":"Single cell sequencing of mild and critical COVID19 PBMC"}]},{"study_accession":"EGAS00001004717","study_title":"Single-cell RNA sequencing of bronchoalveolar lavages from COVID-19 patients","datasets":[{"dataset_accession":"EGAD00001006893","dataset_title":"Single-cell RNA sequencing of bronchoalveolar lavages from COVID-19 patients"}]},{"study_accession":"EGAS00001005304","study_title":"COVID19 Host Genetic Initiative","datasets":[{"dataset_accession":"EGAD00010002171","dataset_title":"Hostage_2_genotype"},{"dataset_accession":"EGAD00010002172","dataset_title":"BRACOVID_genotype"},{"dataset_accession":"EGAD00010002173","dataset_title":"Hostage_3_genotype"},{"dataset_accession":"EGAD00010002174","dataset_title":"INMUNGEN_CoV2_genotype"},{"dataset_accession":"EGAD00010002175","dataset_title":"SweCovid_genotype"},{"dataset_accession":"EGAD00010002177","dataset_title":"GEN_COVID_genotype"},{"dataset_accession":"EGAD00010002178","dataset_title":"Hostage_4_genotype"},{"dataset_accession":"EGAD00010002179","dataset_title":"BelCovid_2_genotype"},{"dataset_accession":"EGAD00010002180","dataset_title":"Hostage_1_genotype"},{"dataset_accession":"EGAD00010002176","dataset_title":"SPGRX_genotype"},{"dataset_accession":"EGAD00001007837","dataset_title":"GEN_COVID_phenotype_lab"},{"dataset_accession":"EGAD00001007844","dataset_title":"Hostage_4_phenotype_basic"},{"dataset_accession":"EGAD00001007832","dataset_title":"BRACOVID_phenotype_basic"},{"dataset_accession":"EGAD00001007850","dataset_title":"SweCovid_phenotype_lab"},{"dataset_accession":"EGAD00001007848","dataset_title":"SPGRX_phenotype_basic"},{"dataset_accession":"EGAD00001007847","dataset_title":"INMUNGEN_CoV2_phenotype_lab"},{"dataset_accession":"EGAD00001007846","dataset_title":"INMUNGEN_CoV2_phenotype_basic"},{"dataset_accession":"EGAD00001007845","dataset_title":"Hostage_4_phenotype_lab"},{"dataset_accession":"EGAD00001007843","dataset_title":"Hostage_3_phenotype_lab"},{"dataset_accession":"EGAD00001007842","dataset_title":"Hostage_3_phenotype_basic"},{"dataset_accession":"EGAD00001007841","dataset_title":"Hostage_2_phenotype_lab"},{"dataset_accession":"EGAD00001007840","dataset_title":"Hostage_2_phenotype_basic"},{"dataset_accession":"EGAD00001007839","dataset_title":"Hostage_1_phenotype_lab"},{"dataset_accession":"EGAD00001007838","dataset_title":"Hostage_1_phenotype_basic"},{"dataset_accession":"EGAD00001007836","dataset_title":"GEN_COVID_phenotype_basic"},{"dataset_accession":"EGAD00001007835","dataset_title":"BelCovid_2_phenotype_lab"},{"dataset_accession":"EGAD00001007834","dataset_title":"BelCovid_2_phenotype_basic"},{"dataset_accession":"EGAD00001007833","dataset_title":"BRACOVID_phenotype_lab"},{"dataset_accession":"EGAD00001007849","dataset_title":"SweCovid_phenotype_basic"}]},{"study_accession":"EGAS00001005461","study_title":"Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children","datasets":[{"dataset_accession":"EGAD00001007969","dataset_title":"Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children"}]},{"study_accession":"EGAS00001004716","study_title":"Ancestry COVID-19 study","datasets":[{"dataset_accession":"EGAD00010002011","dataset_title":"Ancestry COVID-19 Study Phenotype"},{"dataset_accession":"EGAD00010002012","dataset_title":"Ancestry COVID-19 Study Genotype"}]},{"study_accession":"EGAS00001005099","study_title":"AncestryDNA COVID-19 GWAS with Eight Phenotypes","datasets":[{"dataset_accession":"EGAD00010002104","dataset_title":"AncestryDNA COVID-19 GWAS for Continuous_Severity_Score"},{"dataset_accession":"EGAD00010002109","dataset_title":"AncestryDNA COVID-19 GWAS for ExposedPositive_ExposedNegative"},{"dataset_accession":"EGAD00010002111","dataset_title":"AncestryDNA COVID-19 GWAS for Hospitalized_NotHosptialized"},{"dataset_accession":"EGAD00010002120","dataset_title":"AncestryDNA COVID-19 GWAS for Positive_Negative"},{"dataset_accession":"EGAD00010002122","dataset_title":"AncestryDNA COVID-19 GWAS for Symptomatic_Paucisymptomatic"},{"dataset_accession":"EGAD00010002129","dataset_title":"AncestryDNA COVID-19 GWAS for Hospitalized_Unscreened"},{"dataset_accession":"EGAD00010002159","dataset_title":"AncestryDNA COVID-19 GWAS for Positive_Unscreened"},{"dataset_accession":"EGAD00010002162","dataset_title":"AncestryDNA COVID-19 GWAS for Unscreened_ExposedNegative"}]},{"study_accession":"EGAS00001005206","study_title":"High titers and low fucosylation of early phase anti-SARS-CoV-2 IgG promote hyper-inflammation by alveolar macrophages","datasets":[{"dataset_accession":"EGAD00001007512","dataset_title":"anti-SARS-CoV-2 IgG and Fostamatinib treated human primary IL10-M2 macrophages"}]},{"study_accession":"EGAS00001004503","study_title":"Peripheral immunoprofiling of stratifies COVID-19 patients based on disease-specific neutrophil signatures","datasets":[{"dataset_accession":"EGAD00001006671","dataset_title":"Peripheral immunoprofiling of stratifies COVID-19 patients based on disease-specific neutrophil signatures"},{"dataset_accession":"EGAD00001006326","dataset_title":"Peripheral immunoprofiling of stratifies COVID-19 patients based on disease-specific neutrophil signatures"}]},{"study_accession":"EGAS00001004391","study_title":"Paediatric_and_adult_nasal_RNAseq___COVID19","datasets":[{"dataset_accession":"EGAD00001007718","dataset_title":"The cellular immune and airway epithelial profile throughout childhood and in response to COVID-19 at multi-omic single cell level."}]},{"study_accession":"EGAS00001004772","study_title":"Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19","datasets":[{"dataset_accession":"EGAD00001006828","dataset_title":"Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19"}]},{"study_accession":"EGAS00001004481","study_title":"Single-cell analysis of airway samples identifies immune cell activation correlating with COVID-19 disease severity","datasets":[{"dataset_accession":"EGAD00001006339","dataset_title":"COVID-19 severity correlates with airway epithelium\u2013immune cell interactions identified by single-cell analysis"}]},{"study_accession":"EGAS00001004419","study_title":"SARS\u2010CoV\u20102 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells","datasets":[{"dataset_accession":"EGAD00001006185","dataset_title":"ALI culture bronchial cells and alveolar lung surgical resection scRNA-Seq"}]},{"study_accession":"EGAS00001004412","study_title":"Potent neutralizing antibodies against SARS-CoV-2","datasets":[{"dataset_accession":"EGAD00001006130","dataset_title":"Potent neutralizing antibodies against SARS-CoV-2"}]}]}
\ No newline at end of file
i18n/en.toml
View file @ 6f975956
......@@ -280,6 +280,15 @@ other = "Back to top"
[accession_id]
other = "Accession"
["ega_study_accession_id"]
other="Study accession"
["ega_study_title"]
other="Study title"
["datasets_number"]
other="Number of datasets"
[collection_date]
other = "Collection date"
......
layouts/genomics/single.html
View file @ 6f975956
......@@ -57,7 +57,7 @@
<div class="tab-pane fade" id='host-sequences-content' role="tabpanel" aria-labelledby='host-sequences-tab'>
<article>
<h2>Host sequences</h2>
{{ partial "comming-soon.html" }}
{{ partial "genomics/host-sequences-table.html" . }}
</article>
</div>
</div>
......
layouts/partials/genomics/host-sequences-table.html
View file @ 6f975956
......@@ -5,19 +5,17 @@
<table class="table table-hover table-sm table-responsive" id="host-sequences-table" style="display: table;">
<thead class="thead-light">
<tr>
<th scope="col">{{ i18n "accession_id" }}</th>
<th scope="col">{{ i18n "description" }}</th>
<th scope="col">{{ i18n "country" }}</th>
<th scope="col">{{ i18n "region" }}</th>
<th scope="col">{{ i18n "ega_study_accession_id" }}</th>
<th scope="col">{{ i18n "ega_study_title" }}</th>
<th scope="col">{{ i18n "datasets_number" }}</th>
</tr>
</thead>
<tbody>
{{ range $index, $entry := $.Site.Data.c19pes_host_sequences.host_sequences }}
{{ range $index, $entry := $.Site.Data.c19dpes_genomics_host_sequences.ega_studies }}
<tr>
<td><a target="_blank" href='{{print "https://www.ebi.ac.uk/ena/browser/view/" .accession_id}}'>{{ .accession_id }}</a></td>
<td>{{ .description }}</td>
<td>{{ .country }}</td>
<td>{{ .region }}</td>
<td><a target="_blank" href='{{print "https://ega-archive.org/studies/" .study_accession}}'>{{ .study_accession }}</a></td>
<td>{{ .study_title }}</td>
<td>{{ len .datasets }}</td>
</tr>
{{ end }}
</tbody>
......
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