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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T256","span":{"begin":235,"end":240},"obj":"Body_part"},{"id":"T257","span":{"begin":245,"end":249},"obj":"Body_part"},{"id":"T258","span":{"begin":1261,"end":1267},"obj":"Body_part"},{"id":"T259","span":{"begin":1530,"end":1535},"obj":"Body_part"},{"id":"T260","span":{"begin":1606,"end":1610},"obj":"Body_part"}],"attributes":[{"id":"A256","pred":"uberon_id","subj":"T256","obj":"http://purl.obolibrary.org/obo/UBERON_0002116"},{"id":"A257","pred":"uberon_id","subj":"T257","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A258","pred":"uberon_id","subj":"T258","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A259","pred":"uberon_id","subj":"T259","obj":"http://purl.obolibrary.org/obo/UBERON_0002116"},{"id":"A260","pred":"uberon_id","subj":"T260","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"}],"text":"Next, we examined the probability of sequencing an ACE2 transcript as a function of read depth and ACE2’s fractional abundance in each single cell within our sequencing libraries. First, across two different tissues (non-human primate ileum and lung, representing a high expresser of ACE2 and low expresser, respectively), we calculated the proportion of unique ACE2 molecules in our ACE2+ cells (defined as any cell with at least 1 UMI aligning to ACE2) as a fraction of total reads within individual cells to provide an order-of-magnitude estimate for average ACE2 abundance in our single-cell sequencing libraries (i.e., the probability that a read within a cell corresponds to a unique molecule of ACE2, Figure S6B). We highlight that by calculating probabilities based on ACE2 unique molecules divided by an individual cell’s total reads, we are providing a conservative estimate for the probability of observing ACE2 as a function of sequencing depth (e.g., as compared to basing these probabilities on ACE2 non-UMI-collapsed reads divided by total reads). Next, we obtained information on the number of reads in these cell populations to provide estimates of average sequencing depths (Figure S6C). Using the mean fractional abundances of ACE2 from each tissue (Figure S6B) and the mean read depths for all genes (Figure S6C), we calculated the probability of detecting at least 1 ACE2 molecule (i.e., P(detecting \u003e 0 ACE2 molecules) = 1 - (1 - ACE2 fractional abundance)Read depth). This results in a 93.7% probability in ileum-derived cell libraries that contain ACE2, and a 76.0% probability for lung-derived cell libraries, indicating that our sequencing depths are sufficient to detect ACE2+ cells (Figure S6D)."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T18549","span":{"begin":367,"end":376},"obj":"Chemical"},{"id":"T76325","span":{"begin":690,"end":698},"obj":"Chemical"},{"id":"T9827","span":{"begin":789,"end":798},"obj":"Chemical"},{"id":"T1128","span":{"begin":1393,"end":1401},"obj":"Chemical"},{"id":"T15833","span":{"begin":1430,"end":1439},"obj":"Chemical"}],"attributes":[{"id":"A10665","pred":"chebi_id","subj":"T18549","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"},{"id":"A52167","pred":"chebi_id","subj":"T76325","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"},{"id":"A95015","pred":"chebi_id","subj":"T9827","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"},{"id":"A23614","pred":"chebi_id","subj":"T1128","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"},{"id":"A82135","pred":"chebi_id","subj":"T15833","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"}],"text":"Next, we examined the probability of sequencing an ACE2 transcript as a function of read depth and ACE2’s fractional abundance in each single cell within our sequencing libraries. First, across two different tissues (non-human primate ileum and lung, representing a high expresser of ACE2 and low expresser, respectively), we calculated the proportion of unique ACE2 molecules in our ACE2+ cells (defined as any cell with at least 1 UMI aligning to ACE2) as a fraction of total reads within individual cells to provide an order-of-magnitude estimate for average ACE2 abundance in our single-cell sequencing libraries (i.e., the probability that a read within a cell corresponds to a unique molecule of ACE2, Figure S6B). We highlight that by calculating probabilities based on ACE2 unique molecules divided by an individual cell’s total reads, we are providing a conservative estimate for the probability of observing ACE2 as a function of sequencing depth (e.g., as compared to basing these probabilities on ACE2 non-UMI-collapsed reads divided by total reads). Next, we obtained information on the number of reads in these cell populations to provide estimates of average sequencing depths (Figure S6C). Using the mean fractional abundances of ACE2 from each tissue (Figure S6B) and the mean read depths for all genes (Figure S6C), we calculated the probability of detecting at least 1 ACE2 molecule (i.e., P(detecting \u003e 0 ACE2 molecules) = 1 - (1 - ACE2 fractional abundance)Read depth). This results in a 93.7% probability in ileum-derived cell libraries that contain ACE2, and a 76.0% probability for lung-derived cell libraries, indicating that our sequencing depths are sufficient to detect ACE2+ cells (Figure S6D)."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T21","span":{"begin":56,"end":66},"obj":"http://purl.obolibrary.org/obo/GO_0006351"}],"text":"Next, we examined the probability of sequencing an ACE2 transcript as a function of read depth and ACE2’s fractional abundance in each single cell within our sequencing libraries. First, across two different tissues (non-human primate ileum and lung, representing a high expresser of ACE2 and low expresser, respectively), we calculated the proportion of unique ACE2 molecules in our ACE2+ cells (defined as any cell with at least 1 UMI aligning to ACE2) as a fraction of total reads within individual cells to provide an order-of-magnitude estimate for average ACE2 abundance in our single-cell sequencing libraries (i.e., the probability that a read within a cell corresponds to a unique molecule of ACE2, Figure S6B). We highlight that by calculating probabilities based on ACE2 unique molecules divided by an individual cell’s total reads, we are providing a conservative estimate for the probability of observing ACE2 as a function of sequencing depth (e.g., as compared to basing these probabilities on ACE2 non-UMI-collapsed reads divided by total reads). Next, we obtained information on the number of reads in these cell populations to provide estimates of average sequencing depths (Figure S6C). Using the mean fractional abundances of ACE2 from each tissue (Figure S6B) and the mean read depths for all genes (Figure S6C), we calculated the probability of detecting at least 1 ACE2 molecule (i.e., P(detecting \u003e 0 ACE2 molecules) = 1 - (1 - ACE2 fractional abundance)Read depth). This results in a 93.7% probability in ileum-derived cell libraries that contain ACE2, and a 76.0% probability for lung-derived cell libraries, indicating that our sequencing depths are sufficient to detect ACE2+ cells (Figure S6D)."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T855","span":{"begin":0,"end":179},"obj":"Sentence"},{"id":"T856","span":{"begin":180,"end":720},"obj":"Sentence"},{"id":"T857","span":{"begin":721,"end":1062},"obj":"Sentence"},{"id":"T858","span":{"begin":1063,"end":1205},"obj":"Sentence"},{"id":"T859","span":{"begin":1206,"end":1490},"obj":"Sentence"},{"id":"T860","span":{"begin":1491,"end":1723},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Next, we examined the probability of sequencing an ACE2 transcript as a function of read depth and ACE2’s fractional abundance in each single cell within our sequencing libraries. First, across two different tissues (non-human primate ileum and lung, representing a high expresser of ACE2 and low expresser, respectively), we calculated the proportion of unique ACE2 molecules in our ACE2+ cells (defined as any cell with at least 1 UMI aligning to ACE2) as a fraction of total reads within individual cells to provide an order-of-magnitude estimate for average ACE2 abundance in our single-cell sequencing libraries (i.e., the probability that a read within a cell corresponds to a unique molecule of ACE2, Figure S6B). We highlight that by calculating probabilities based on ACE2 unique molecules divided by an individual cell’s total reads, we are providing a conservative estimate for the probability of observing ACE2 as a function of sequencing depth (e.g., as compared to basing these probabilities on ACE2 non-UMI-collapsed reads divided by total reads). Next, we obtained information on the number of reads in these cell populations to provide estimates of average sequencing depths (Figure S6C). Using the mean fractional abundances of ACE2 from each tissue (Figure S6B) and the mean read depths for all genes (Figure S6C), we calculated the probability of detecting at least 1 ACE2 molecule (i.e., P(detecting \u003e 0 ACE2 molecules) = 1 - (1 - ACE2 fractional abundance)Read depth). This results in a 93.7% probability in ileum-derived cell libraries that contain ACE2, and a 76.0% probability for lung-derived cell libraries, indicating that our sequencing depths are sufficient to detect ACE2+ cells (Figure S6D)."}

LitCovid-PubTator