PMC:7417788 / 74655-75329
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7417788","sourcedb":"PMC","sourceid":"7417788","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7417788","text":"scATAC-seq targeting 4,000 cells per sample was performed using Chromium Single Cell ATAC Library and Gel Bead kit (10x Genomics, 1000110). Each sample library was uniquely barcoded and quantified by RT-qPCR. Libraries were then pooled and loaded on an Illumina Novaseq 6000 sequencer (3.5 pmol/L loading concentration, 50 + 8 + 16 + 49 bp read configuration) and sequenced to either 90% saturation or 30,000 unique reads per cell on average. All protocols to generate scATAC-seq data on the 10x Chromium platform, including sample preparation, library preparation and instrument and sequencing settings, are available here: https://support.10xgenomics.com/single-cell-atac.","tracks":[{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T1509","span":{"begin":64,"end":72},"obj":"CHEBI:28073;CHEBI:28073"},{"id":"T1510","span":{"begin":337,"end":339},"obj":"SO:0000028"},{"id":"T1511","span":{"begin":416,"end":421},"obj":"SO:0000150"},{"id":"T1512","span":{"begin":496,"end":504},"obj":"CHEBI:28073;CHEBI:28073"}],"attributes":[{"subj":"T1509","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T1510","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T1511","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T1512","pred":"source","obj":"LitCovid-PMC-OGER-BB"}]},{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T549","span":{"begin":27,"end":32},"obj":"Body_part"},{"id":"T550","span":{"begin":80,"end":84},"obj":"Body_part"},{"id":"T551","span":{"begin":426,"end":430},"obj":"Body_part"},{"id":"T552","span":{"begin":664,"end":668},"obj":"Body_part"}],"attributes":[{"id":"A549","pred":"fma_id","subj":"T549","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A550","pred":"fma_id","subj":"T550","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A551","pred":"fma_id","subj":"T551","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A552","pred":"fma_id","subj":"T552","obj":"http://purl.org/sig/ont/fma/fma68646"},{"subj":"T549","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T550","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T551","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T552","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T1205","span":{"begin":27,"end":32},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1206","span":{"begin":80,"end":84},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1207","span":{"begin":422,"end":430},"obj":"http://purl.obolibrary.org/obo/CLO_0008190"},{"id":"T1208","span":{"begin":569,"end":579},"obj":"http://purl.obolibrary.org/obo/OBI_0000968"},{"id":"T1209","span":{"begin":664,"end":668},"obj":"http://purl.obolibrary.org/obo/GO_0005623"}],"attributes":[{"subj":"T1205","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1206","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1207","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1208","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1209","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T92477","span":{"begin":64,"end":72},"obj":"Chemical"},{"id":"T39474","span":{"begin":496,"end":504},"obj":"Chemical"}],"attributes":[{"id":"A28958","pred":"chebi_id","subj":"T92477","obj":"http://purl.obolibrary.org/obo/CHEBI_28073"},{"id":"A4454","pred":"chebi_id","subj":"T39474","obj":"http://purl.obolibrary.org/obo/CHEBI_28073"},{"subj":"T92477","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T39474","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T424","span":{"begin":0,"end":139},"obj":"Sentence"},{"id":"T425","span":{"begin":140,"end":208},"obj":"Sentence"},{"id":"T426","span":{"begin":209,"end":442},"obj":"Sentence"},{"id":"T427","span":{"begin":443,"end":674},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T424","pred":"source","obj":"LitCovid-sentences"},{"subj":"T425","pred":"source","obj":"LitCovid-sentences"},{"subj":"T426","pred":"source","obj":"LitCovid-sentences"},{"subj":"T427","pred":"source","obj":"LitCovid-sentences"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"1502","span":{"begin":111,"end":114},"obj":"Gene"},{"id":"1503","span":{"begin":496,"end":504},"obj":"Chemical"}],"attributes":[{"id":"A1502","pred":"tao:has_database_id","subj":"1502","obj":"Gene:3815"},{"id":"A1503","pred":"tao:has_database_id","subj":"1503","obj":"MESH:D002857"},{"subj":"1502","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1503","pred":"source","obj":"LitCovid-PubTator"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PMC-OGER-BB","color":"#93ece5","default":true},{"id":"LitCovid-PD-FMA-UBERON","color":"#eccb93"},{"id":"LitCovid-PD-CLO","color":"#b093ec"},{"id":"LitCovid-PD-CHEBI","color":"#93ec96"},{"id":"LitCovid-sentences","color":"#ec93a9"},{"id":"LitCovid-PubTator","color":"#93c3ec"}]}]}}