LitCovid-sentences  

PMC:7252096 / 73383-79504 JSONTXT 11 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T466 0-37 Sentence denotes REAGENT or RESOURCE SOURCE IDENTIFIER
T467 38-56 Sentence denotes Biological Samples
T468 57-254 Sentence denotes M. mulatta lung, bone marrow, brain, colon, ileum, jejunum, liver, lung, peripheral blood, spleen, thymus, tonsil, and lymph nodes from various sites Washington National Primate Research Center N/A
T469 255-339 Sentence denotes Human lung tissue from surgical excess University of KwaZulu-Natal IRB Code:BE024/09
T470 340-504 Sentence denotes Human non-inflamed ileal pinch biopsies Multi-center clinical study, approved by the Institutional Review Board at Boston Children’s Hospital IRB Code:IRB-P00030890
T471 505-570 Sentence denotes Human nasal lavage University of Massachusetts Medical School N/A
T472 571-681 Sentence denotes Human nasal scraping, polyp scrapings, ethmoid sinus surgical tissue samples Partners HealthCare Institute N/A
T473 682-775 Sentence denotes M. fascicularis lung and granulomatous tissue University of Pittsburgh School of Medicine N/A
T474 776-786 Sentence denotes Antibodies
T475 787-842 Sentence denotes anti-ACE2 human antibody, goat polyclonal R&D Cat#AF933
T476 843-870 Sentence denotes Bacterial and Virus Strains
T477 871-900 Sentence denotes MHV-68 Adler et al., 2000 N/A
T478 901-975 Sentence denotes Mycobacterium Tuberculosis, Modified Erdman Strain Martin et al., 2017 N/A
T479 976-1021 Sentence denotes Chemicals, Peptides, and Recombinant Proteins
T480 1022-1060 Sentence denotes 2-Mercaptoethanol Sigma Cat#M3148-25ML
T481 1061-1088 Sentence denotes RLT Buffer QIAGEN Cat#79216
T482 1089-1124 Sentence denotes dNTP New England BioLabs Cat#N0447L
T483 1125-1169 Sentence denotes RNase Inhibitor Fisher Scientific Cat#AM2696
T484 1170-1228 Sentence denotes Maxima RNaseH-minus RT Enzyme Fisher Scientific Cat#EP0753
T485 1229-1256 Sentence denotes MgCl2 Sigma Cat#63069-100ML
T486 1257-1284 Sentence denotes Betaine Sigma Cat#B0300-5VL
T487 1285-1345 Sentence denotes AMPure RNAClean XP RNA-SPRI beads Beckman Coulter Cat#A63987
T488 1346-1393 Sentence denotes AMPure XP SPRI beads Beckman Coulter Cat#A63881
T489 1394-1434 Sentence denotes Guanidinium thiocyanate Sigma Cat#AM9422
T490 1435-1459 Sentence denotes Sarkosyl Sigma Cat#L7414
T491 1460-1504 Sentence denotes Exonuclease I New England BioLabs Cat#M0293S
T492 1505-1551 Sentence denotes Klenow Fragment New England BioLabs Cat#M0212L
T493 1552-1581 Sentence denotes DNase I Roche Cat#10104159001
T494 1582-1627 Sentence denotes Collagenase IV Life Technologies Cat#17104019
T495 1628-1663 Sentence denotes Collagenase D Roche Cat#11088858001
T496 1664-1696 Sentence denotes Liberase TM Roche Cat#5401119001
T497 1697-1730 Sentence denotes TrypLE Thermo Fisher Cat#12604013
T498 1731-1768 Sentence denotes ACK Buffer Thermo Fisher Cat#A1049201
T499 1769-1795 Sentence denotes IFN-α Biolegend Cat#752802
T500 1796-1833 Sentence denotes Dispase II Thermo Fisher Cat#17105041
T501 1834-1875 Sentence denotes Elastase Worthington Biochem Cat#LS002292
T502 1876-1934 Sentence denotes Pneumacult-Ex serum-free media StemCell Technologies, Inc.
T503 1935-1944 Sentence denotes Cat#05040
T504 1945-1977 Sentence denotes IL-4, human Biolegend Cat#574002
T505 1978-2011 Sentence denotes IL17A, human Biolegend Cat#570502
T506 2012-2044 Sentence denotes IFNγ, human Biolegend Cat#570202
T507 2045-2077 Sentence denotes IFNγ, mouse Peprotech Cat#315-05
T508 2078-2110 Sentence denotes IFNα, human Biolegend Cat#592702
T509 2111-2143 Sentence denotes IFNα, mouse Biolegend Cat#752802
T510 2144-2183 Sentence denotes IFNβ, mouse R&D Systems Cat#8234-MB-010
T511 2184-2210 Sentence denotes Critical Commercial Assays
T512 2211-2274 Sentence denotes Nextera XT DNA Library Preparation Kit Illumina Cat#FC-131-1096
T513 2275-2330 Sentence denotes High Sensitivity D5000 ScreenTape Agilent Cat#5067-5592
T514 2331-2387 Sentence denotes Qubit dsDNA High-Sensitivity kit ThermoFisher Cat#Q32854
T515 2388-2455 Sentence denotes NextSeq 500/550 High Output v2 (75 cycles) Illumina Cat#FC-404-2005
T516 2456-2506 Sentence denotes NovaSeq 6000 S2 (100 cycles) Illumina Cat#20012862
T517 2507-2561 Sentence denotes Kapa HiFi HotStart ReadyMix Kapa Biosystems Cat#KK2602
T518 2562-2620 Sentence denotes MACOSKO-2011-10 mRNA Capture Beads ChemGenes Cat#NC0927472
T519 2621-2682 Sentence denotes Tumor Dissociation Kit, Human Miltenyi Biotec Cat#130-095-929
T520 2683-2733 Sentence denotes Chromium Single Cell 3′ v2 10X Genomics Cat#120237
T521 2734-2748 Sentence denotes Deposited Data
T522 2749-2863 Sentence denotes scRNA-seq Processed Data This paper https://singlecell.broadinstitute.org/single_cell?scpbr=the-alexandria-project
T523 2864-2984 Sentence denotes scRNA-seq Processed Data This paper https://drive.google.com/drive/folders/1bxCIqNeZ7wLuVOT16gphwj98_cc9KhrV?usp=sharing
T524 2985-3094 Sentence denotes scRNA-seq Processed Data This paper https://chanzuckerberg.github.io/cellxgene/posts/cellxgene_cziscience_com
T525 3095-3188 Sentence denotes scRNA-seq Processed Data This paper https://singlecell.broadinstitute.org/single_cell/covid19
T526 3189-3299 Sentence denotes scRNA-seq Processed Data (all species) and FASTQ files (for NHP and murine datasets) This paper GEO: GSE148829
T527 3300-3509 Sentence denotes scRNA-seq data from human nasal mucosa Ordovas-Montanes et al., 2018 https://singlecell.broadinstitute.org/single_cell/study/SCP253/allergic-inflammatory-memory-in-human-respiratory-epithelial-progenitor-cells
T528 3510-3647 Sentence denotes Human reference genome NCBI build 38 (GRCh38) Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
T529 3648-3776 Sentence denotes Human reference genome NCBI build 19 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
T530 3777-3905 Sentence denotes Mouse reference genome NCBI build 10 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/
T531 3906-4082 Sentence denotes Macaca mulatta reference genome assembly 8.0.1, annotation 102 NCBI Eukaryotic Genome Annotation Pipeline https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Macaca_mulatta/102/
T532 4083-4265 Sentence denotes Macaca fascicularis reference genome assembly 5, annotation 101 NCBI Eukaryotic Genome Annotation Pipeline https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Macaca_fascicularis/101/
T533 4266-4336 Sentence denotes Interferome Database Rusinova et al., 2013 http://www.interferome.org/
T534 4337-4427 Sentence denotes RNA-seq from human lung explants ± ex vivo IAV infection Matos et al., 2019 GEO: GSE135069
T535 4428-4523 Sentence denotes RNA-seq from human nasal epithelial cells Giovannini-Chami et al., 2012 GEO: GSE19190, GSE22147
T536 4524-4544 Sentence denotes Experimental Models:
T537 4545-4555 Sentence denotes Cell Lines
T538 4556-4562 Sentence denotes Human:
T539 4563-4594 Sentence denotes Passage 4 BEAS-2B ATCC CRL-9609
T540 4595-4615 Sentence denotes Experimental Models:
T541 4616-4633 Sentence denotes Organisms/Strains
T542 4634-4683 Sentence denotes Mouse: C57BL/6J The Jackson Laboratory Cat#000664
T543 4684-4766 Sentence denotes Mouse: C57BL/6, IFNγR−/− B6.129S7-Ifngr1tm1Agt/J The Jackson Laboratory Cat#003288
T544 4767-4783 Sentence denotes Oligonucleotides
T545 4784-4932 Sentence denotes SMART-seq2 2 3′ Oligo-dT Primer: /5Biosg/AAG CAG TGG TAT CAA CGC AGA GTA CTT TTT TTT TTT TTT TTT TTT TTT TTT TTT TVN Integrated DNA Technologies N/A
T546 4933-5026 Sentence denotes SMART-seq2 5′ TSO: AAG CAG TGG TAT CAA CGC AGA GTA CAT rGrGrG Integrated DNA Technologies N/A
T547 5027-5119 Sentence denotes SMART-seq2 and Seq-Well ISPCR:AAG CAG TGG TAT CAA CGC AGA GT Integrated DNA Technologies N/A
T548 5120-5223 Sentence denotes Custom Read 1 Primer: GCC TGT CCG CGG AAG CAG TGG TAT CAA CGC AGA GTA C Integrated DNA Technologies N/A
T549 5224-5315 Sentence denotes Seq-Well 5′ TSO: AAG CAG TGG TAT CAA CGC AGA GTG AAT rGrGrG Integrated DNA Technologies N/A
T550 5316-5478 Sentence denotes Seq-Well Custom P5-SMART PCR hybrid oligo: AAT GAT ACG GCG ACC ACC GAG ATC TAC ACG CCT GTC CGC GGA AGC AGT GGT ATC AAC GCA GAG TAC Integrated DNA Technologies N/A
T551 5479-5580 Sentence denotes Seq-Well dN-SMRT oligo: AAG CAG TGG TAT CAA CGC AGA GTG ANN NGG NNN B Integrated DNA Technologies N/A
T552 5581-5604 Sentence denotes Software and Algorithms
T553 5605-5644 Sentence denotes R R Core Team https://www.r-project.org
T554 5645-5724 Sentence denotes R package – Seurat v2.3.4 and v3.1.0 Github https://github.com/satijalab/seurat
T555 5725-5784 Sentence denotes Scanpy Wolf et al., 2018 https://github.com/theislab/scanpy
T556 5785-5853 Sentence denotes R package – SCDE Bioconductor http://bioconductor.org/packages/scde/
T557 5854-5931 Sentence denotes Prism 6 GraphPad Software https://www.graphpad.com/scientific-software/prism/
T558 5932-5977 Sentence denotes STAR Github https://github.com/alexdobin/STAR
T559 5978-6063 Sentence denotes Uniform Manifold Approximation and Projection Github https://github.com/lmcinnes/umap
T560 6064-6121 Sentence denotes Rtsne CRAN https://cran.r-project.org/web/packages/Rtsne/