Improving oligo-conjugated antibody signal in multimodal single-cell analysis
Simultaneous measurement of surface proteins and gene expression within single cells using oligo-conjugated antibodies offers high-resolution snapshots of complex cell populations. Signal from oligo-conjugated antibodies is quantified by high-throughput sequencing and is highly scalable and sensitiv...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications Ltd
2021-04-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/61973 |
| _version_ | 1828376018246696960 |
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| author | Terkild B Buus Alberto Herrera Ellie Ivanova Eleni Mimitou Anthony Cheng Ramin S Herati Thales Papagiannakopoulos Peter Smibert Niels Odum Sergei B Koralov |
| author_facet | Terkild B Buus Alberto Herrera Ellie Ivanova Eleni Mimitou Anthony Cheng Ramin S Herati Thales Papagiannakopoulos Peter Smibert Niels Odum Sergei B Koralov |
| author_sort | Terkild B Buus |
| collection | DOAJ |
| description | Simultaneous measurement of surface proteins and gene expression within single cells using oligo-conjugated antibodies offers high-resolution snapshots of complex cell populations. Signal from oligo-conjugated antibodies is quantified by high-throughput sequencing and is highly scalable and sensitive. We investigated the response of oligo-conjugated antibodies towards four variables: concentration, staining volume, cell number at staining, and tissue. We find that staining with recommended antibody concentrations causes unnecessarily high background and amount of antibody used can be drastically reduced without loss of biological information. Reducing staining volume only affects antibodies targeting abundant epitopes used at low concentrations and is counteracted by reducing cell numbers. Adjusting concentrations increases signal, lowers background, and reduces costs. Background signal can account for a major fraction of total sequencing and is primarily derived from antibodies used at high concentrations. This study provides new insight into titration response and background of oligo-conjugated antibodies and offers concrete guidelines to improve such panels. |
| first_indexed | 2024-04-14T07:54:32Z |
| format | Article |
| id | doaj.art-2bc6f48722e04927b6f51a7d848b2bfb |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-14T07:54:32Z |
| publishDate | 2021-04-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-2bc6f48722e04927b6f51a7d848b2bfb2022-12-22T02:05:06ZengeLife Sciences Publications LtdeLife2050-084X2021-04-011010.7554/eLife.61973Improving oligo-conjugated antibody signal in multimodal single-cell analysisTerkild B Buus0https://orcid.org/0000-0001-7180-6384Alberto Herrera1https://orcid.org/0000-0003-4189-9051Ellie Ivanova2https://orcid.org/0000-0002-1850-9505Eleni Mimitou3https://orcid.org/0000-0001-9737-6394Anthony Cheng4https://orcid.org/0000-0002-0778-8238Ramin S Herati5https://orcid.org/0000-0003-2613-4050Thales Papagiannakopoulos6https://orcid.org/0000-0002-2251-1624Peter Smibert7https://orcid.org/0000-0003-0772-1647Niels Odum8https://orcid.org/0000-0003-3135-5624Sergei B Koralov9https://orcid.org/0000-0002-4843-3791Department of Pathology, New York University School of Medicine, New York, United States; LEO Foundation Skin Immunology Research Center, University of Copenhagen, Copenhagen, Denmark; Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, DenmarkDepartment of Pathology, New York University School of Medicine, New York, United StatesDepartment of Pathology, New York University School of Medicine, New York, United StatesTechnology Innovation Lab, New York Genome Center, New York, United StatesDepartment of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, United States; Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, United StatesNYU Langone Vaccine Center, Department of Medicine, New York University School of Medicine, New York, United StatesDepartment of Pathology, New York University School of Medicine, New York, United StatesTechnology Innovation Lab, New York Genome Center, New York, United StatesLEO Foundation Skin Immunology Research Center, University of Copenhagen, Copenhagen, Denmark; Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, DenmarkDepartment of Pathology, New York University School of Medicine, New York, United StatesSimultaneous measurement of surface proteins and gene expression within single cells using oligo-conjugated antibodies offers high-resolution snapshots of complex cell populations. Signal from oligo-conjugated antibodies is quantified by high-throughput sequencing and is highly scalable and sensitive. We investigated the response of oligo-conjugated antibodies towards four variables: concentration, staining volume, cell number at staining, and tissue. We find that staining with recommended antibody concentrations causes unnecessarily high background and amount of antibody used can be drastically reduced without loss of biological information. Reducing staining volume only affects antibodies targeting abundant epitopes used at low concentrations and is counteracted by reducing cell numbers. Adjusting concentrations increases signal, lowers background, and reduces costs. Background signal can account for a major fraction of total sequencing and is primarily derived from antibodies used at high concentrations. This study provides new insight into titration response and background of oligo-conjugated antibodies and offers concrete guidelines to improve such panels.https://elifesciences.org/articles/61973CITE-seqECCITE-seqscRNA-seqcytometryoligo-conjugated antibodiesBackground signal |
| spellingShingle | Terkild B Buus Alberto Herrera Ellie Ivanova Eleni Mimitou Anthony Cheng Ramin S Herati Thales Papagiannakopoulos Peter Smibert Niels Odum Sergei B Koralov Improving oligo-conjugated antibody signal in multimodal single-cell analysis eLife CITE-seq ECCITE-seq scRNA-seq cytometry oligo-conjugated antibodies Background signal |
| title | Improving oligo-conjugated antibody signal in multimodal single-cell analysis |
| title_full | Improving oligo-conjugated antibody signal in multimodal single-cell analysis |
| title_fullStr | Improving oligo-conjugated antibody signal in multimodal single-cell analysis |
| title_full_unstemmed | Improving oligo-conjugated antibody signal in multimodal single-cell analysis |
| title_short | Improving oligo-conjugated antibody signal in multimodal single-cell analysis |
| title_sort | improving oligo conjugated antibody signal in multimodal single cell analysis |
| topic | CITE-seq ECCITE-seq scRNA-seq cytometry oligo-conjugated antibodies Background signal |
| url | https://elifesciences.org/articles/61973 |
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