CITE-seq data from Staphylococcus aureus induce drug resistance in cancer T cells in Sézary Syndrome Article Swipe
Terkild B. Buus
,
Chella Krishna Vadivel
,
Niels Ødum
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.6084/m9.figshare.23649780
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.6084/m9.figshare.23649780
CITE-seq dataset of cells from a Sézary Syndrome patient cultured in the presence or absence of Romidepsin and/or S. aureus enterotoxins (SE) used in article:Chella Krishna Vadivel, Andreas Willerslev-Olsen, Martin Rich Javadi Namini, Ziao Zeng, Lang Yan, Maria Danielsen, Maria Gluud, Emil Marek Heymans Pallesen, Karolina Wojewoda, Amra Osmancevic, Signe Hedebo, Yun-Tsan Chang, Lise M. Lindahl, Sergei B. Koralov, Larisa J Geskin, Susan E Bates, Lars Iversen, Thomas Litman, Rikke Bech, Marion Wobser, Emmanuella Guenova, Maria R. Kamstrup, Niels Odum*, Terkild B. Buus*; Staphylococcus aureus induce drug resistance in cancer T cells in Sézary Syndrome. Blood 2024; blood.2023021671. DOI: https://doi.org/10.1182/blood.2023021671SS17.rds is contains R Data Serialization (RDS) file of a SingleCellExperiment (SCE) R object containing integrated single-cell CITE-seq data from four samples (PBS, Romidepsin, SE and Romidepsin+SE treatment) after 36 hours of in vitro culture.The column data (colData) of the SCE object contains the following information from each cell:treatment - whether cell was cultured in the presence (Romidepsin) or absence (DMSO) of Romidepsinstimulation - whether cell was cultured in the presence (SE) or absence (PBS) of S. aureus enterotoxins (SE)group - cell sample condition origin (a combination of stimulation and treatment columns)lane - whether cell was included in lane1 or lane2 of the two 10X Chromium lanes run in parallel from the same cell suspension poolsum - number of Unique Molecular Identifiers (UMIs) assigned to the celldetected - number of genes detected in the cellsubsets_Mito_percent - proportion of UMIs stemming from mitochondrial genessizeFactor - calculated sizeFactor for normalizationTRA_top5 - assignment of TCRalpha chain clonotype to one of the top5 clonotypes detected based on CDR3 amino acid sequenceTRB_top5 - assignment of TCRbeta chain clonotype to one of the top5 clonotypes detected based on CDR3 amino acid sequencecc_phase - inferred cell cycle phasecc_score_s - inferred cell cycle S-phase scorecc_score_G2M - inferred cell cycle G2M-phase scoreleiden_totalVI - leiden clustering assignment from lantent space of totalVI runcell_type - Cell type assignment of the cellSCE object contains three alternative experiment objects:ADT - Antibody derived tag (ADT) UMI counts from surface protein modalityVI_ADT - Antibody derived tag (ADT) UMI counts from surface protein modality denoised and normalized by totalVITF - Transcription factor activation scores (from DoRothEA) for each cell calculated using decoupleRSCE object contains three dimension reductions:PCA - principal component analysis calculated based on highly variable genestotalVI - latent space loadings from totalVI analysisumap - Uniform Manifold Approximation and Projection calculated based on latent space from totalVICode used in the analysis of this data is available on GitHub
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Metadata
- Type
- dataset
- Language
- en
- Landing Page
- https://doi.org/10.6084/m9.figshare.23649780
- OA Status
- gold
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- 10
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- https://openalex.org/W4394174825
All OpenAlex metadata
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https://openalex.org/W4394174825Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.6084/m9.figshare.23649780Digital Object Identifier
- Title
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CITE-seq data from Staphylococcus aureus induce drug resistance in cancer T cells in Sézary SyndromeWork title
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datasetOpenAlex work type
- Language
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enPrimary language
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2024Year of publication
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2024-01-01Full publication date if available
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Terkild B. Buus, Chella Krishna Vadivel, Niels ØdumList of authors in order
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https://doi.org/10.6084/m9.figshare.23649780Publisher landing page
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://doi.org/10.6084/m9.figshare.23649780Direct OA link when available
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Staphylococcus aureus, Drug resistance, Multi drug resistant, B cell, Microbiology, Cancer, Medicine, Cancer research, Biology, Immunology, Bacteria, Antibody, Genetics, Internal medicineTop concepts (fields/topics) attached by OpenAlex
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0Total citation count in OpenAlex
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.whether | 149, 163, 192 |
| abstract_inverted_index.<i>Blood | 95 |
| abstract_inverted_index.Antibody | 326, 337 |
| abstract_inverted_index.CITE-seq | 0, 116 |
| abstract_inverted_index.Chromium | 204 |
| abstract_inverted_index.Guenova, | 74 |
| abstract_inverted_index.Iversen, | 66 |
| abstract_inverted_index.Karolina | 45 |
| abstract_inverted_index.Koralov, | 58 |
| abstract_inverted_index.Lindahl, | 55 |
| abstract_inverted_index.Manifold | 389 |
| abstract_inverted_index.Syndrome | 7 |
| abstract_inverted_index.TCRalpha | 250 |
| abstract_inverted_index.Vadivel, | 26 |
| abstract_inverted_index.Yun-Tsan | 51 |
| abstract_inverted_index.analysis | 373, 403 |
| abstract_inverted_index.assigned | 222 |
| abstract_inverted_index.contains | 101, 141, 320, 366 |
| abstract_inverted_index.cultured | 9, 152, 166 |
| abstract_inverted_index.denoised | 347 |
| abstract_inverted_index.detected | 230, 259, 278 |
| abstract_inverted_index.included | 195 |
| abstract_inverted_index.inferred | 286, 291, 297 |
| abstract_inverted_index.loadings | 383 |
| abstract_inverted_index.modality | 346 |
| abstract_inverted_index.parallel | 208 |
| abstract_inverted_index.presence | 12, 155, 169 |
| abstract_inverted_index.stemming | 238 |
| abstract_inverted_index.variable | 378 |
| abstract_inverted_index.(SE)group | 178 |
| abstract_inverted_index.<i>column | 134 |
| abstract_inverted_index.DoRothEA) | 358 |
| abstract_inverted_index.G2M-phase | 300 |
| abstract_inverted_index.Kamstrup, | 77 |
| abstract_inverted_index.Molecular | 219 |
| abstract_inverted_index.Pallesen, | 44 |
| abstract_inverted_index.Wojewoda, | 46 |
| abstract_inverted_index.available | 408 |
| abstract_inverted_index.clonotype | 252, 271 |
| abstract_inverted_index.component | 372 |
| abstract_inverted_index.condition | 182 |
| abstract_inverted_index.following | 143 |
| abstract_inverted_index.principal | 371 |
| abstract_inverted_index.totalVITF | 351 |
| abstract_inverted_index.treatment | 189 |
| abstract_inverted_index.Danielsen, | 38 |
| abstract_inverted_index.Emmanuella | 73 |
| abstract_inverted_index.Projection | 392 |
| abstract_inverted_index.Romidepsin | 16 |
| abstract_inverted_index.activation | 355 |
| abstract_inverted_index.assignment | 248, 267, 305, 315 |
| abstract_inverted_index.calculated | 243, 362, 374, 393 |
| abstract_inverted_index.clonotypes | 258, 277 |
| abstract_inverted_index.clustering | 304 |
| abstract_inverted_index.containing | 113 |
| abstract_inverted_index.experiment | 323 |
| abstract_inverted_index.integrated | 114 |
| abstract_inverted_index.normalized | 349 |
| abstract_inverted_index.proportion | 235 |
| abstract_inverted_index.resistance | 87 |
| abstract_inverted_index.sizeFactor | 244 |
| abstract_inverted_index.suspension | 213 |
| abstract_inverted_index.treatment) | 126 |
| abstract_inverted_index.Identifiers | 220 |
| abstract_inverted_index.Osmancevic, | 48 |
| abstract_inverted_index.Romidepsin, | 122 |
| abstract_inverted_index.combination | 185 |
| abstract_inverted_index.culture.The | 133 |
| abstract_inverted_index.information | 144 |
| abstract_inverted_index.single-cell | 115 |
| abstract_inverted_index.stimulation | 187 |
| abstract_inverted_index.totalVICode | 399 |
| abstract_inverted_index.(Romidepsin) | 156 |
| abstract_inverted_index.<i>dimension | 368 |
| abstract_inverted_index.analysisumap | 386 |
| abstract_inverted_index.celldetected | 225 |
| abstract_inverted_index.columns)lane | 190 |
| abstract_inverted_index.decoupleRSCE | 364 |
| abstract_inverted_index.enterotoxins | 20, 177 |
| abstract_inverted_index.genestotalVI | 379 |
| abstract_inverted_index.runcell_type | 311 |
| abstract_inverted_index.</i>(colData) | 136 |
| abstract_inverted_index.Approximation | 390 |
| abstract_inverted_index.Romidepsin+SE | 125 |
| abstract_inverted_index.Serialization | 104 |
| abstract_inverted_index.Syndrome</b>. | 94 |
| abstract_inverted_index.Transcription | 353 |
| abstract_inverted_index.mitochondrial | 240 |
| abstract_inverted_index.<i>alternative | 322 |
| abstract_inverted_index.article:Chella | 24 |
| abstract_inverted_index.cell:treatment | 147 |
| abstract_inverted_index.modalityVI_ADT | 335 |
| abstract_inverted_index.</i>objects:ADT | 324 |
| abstract_inverted_index.genessizeFactor | 241 |
| abstract_inverted_index.phasecc_score_s | 289 |
| abstract_inverted_index.sequenceTRB_top5 | 265 |
| abstract_inverted_index.sequencecc_phase | 284 |
| abstract_inverted_index.<b>Staphylococcus | 83 |
| abstract_inverted_index.Willerslev-Olsen, | 28 |
| abstract_inverted_index.scorecc_score_G2M | 295 |
| abstract_inverted_index.reductions</i>:PCA | 369 |
| abstract_inverted_index.scoreleiden_totalVI | 301 |
| abstract_inverted_index.SingleCellExperiment | 109 |
| abstract_inverted_index.Romidepsinstimulation | 161 |
| abstract_inverted_index.blood.2023021671.</i> | 97 |
| abstract_inverted_index.normalizationTRA_top5 | 246 |
| abstract_inverted_index.cellsubsets_Mito_percent | 233 |
| abstract_inverted_index.https://doi.org/10.1182/blood.2023021671SS17.rds | 99 |
| cited_by_percentile_year | |
| countries_distinct_count | 0 |
| institutions_distinct_count | 3 |
| citation_normalized_percentile |