A dataset examining technical factors on fixed white blood cell single-cell RNA-seqGene expression Omnibus
Single-cell RNA sequencing (scRNA-seq) is a powerful technology that enables the measurement of gene expression in individual cells. Such precision provides insights into cellular heterogeneity that bulk methods might overlook. Fragile cells, in particular neutrophils, have posed significant challen...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-12-01
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| Series: | Data in Brief |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352340924010588 |
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| author | Daniel V Brown Agnieszka Swierczak Yue You Yupei You Daniela Amann-Zalcenstein Peter Hickey Arthur Hsu Matthew E. Ritchie Monther Alhamdoosh Judith Field Rory Bowden |
| author_facet | Daniel V Brown Agnieszka Swierczak Yue You Yupei You Daniela Amann-Zalcenstein Peter Hickey Arthur Hsu Matthew E. Ritchie Monther Alhamdoosh Judith Field Rory Bowden |
| author_sort | Daniel V Brown |
| collection | DOAJ |
| description | Single-cell RNA sequencing (scRNA-seq) is a powerful technology that enables the measurement of gene expression in individual cells. Such precision provides insights into cellular heterogeneity that bulk methods might overlook. Fragile cells, in particular neutrophils, have posed significant challenges for scRNA-Seq due to their ex vivo fragility, high RNase content and consequent loss during cryopreservation. The introduction of fixed scRNA-Seq methodology offers a promising solution to these challenges. We evaluated the performance of two different commercial platforms on red blood cell-depleted whole blood cells: 10x Genomics Flex v1 and Honeycomb HIVE v1.These data are publicly available from the Gene Expression Omnibus database (accession number GSE266615).Further insights could be gained by correcting batch and technical effects introduced by storage time after fixation and cell numbers fixed. These data may be used to examine how reflective the transcriptome of neutrophils are of the native environment. |
| format | Article |
| id | doaj-art-f5257f530f9f48c0ae156d3e0fe3d9b5 |
| institution | Kabale University |
| issn | 2352-3409 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Data in Brief |
| spelling | doaj-art-f5257f530f9f48c0ae156d3e0fe3d9b52024-11-18T04:33:20ZengElsevierData in Brief2352-34092024-12-0157111096A dataset examining technical factors on fixed white blood cell single-cell RNA-seqGene expression OmnibusDaniel V Brown0Agnieszka Swierczak1Yue You2Yupei You3Daniela Amann-Zalcenstein4Peter Hickey5Arthur Hsu6Matthew E. Ritchie7Monther Alhamdoosh8Judith Field9Rory Bowden10The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Corresponding author.CSL Innovation, Bio21 Institute, Parkville VIC, AustraliaThe Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Guangzhou National Laboratory, Guangzhou, ChinaThe Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, AustraliaThe Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, AustraliaThe Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, AustraliaCSL Innovation, Bio21 Institute, Parkville VIC, AustraliaThe Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, AustraliaCSL Innovation, Bio21 Institute, Parkville VIC, AustraliaCSL Innovation, Bio21 Institute, Parkville VIC, AustraliaThe Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, AustraliaSingle-cell RNA sequencing (scRNA-seq) is a powerful technology that enables the measurement of gene expression in individual cells. Such precision provides insights into cellular heterogeneity that bulk methods might overlook. Fragile cells, in particular neutrophils, have posed significant challenges for scRNA-Seq due to their ex vivo fragility, high RNase content and consequent loss during cryopreservation. The introduction of fixed scRNA-Seq methodology offers a promising solution to these challenges. We evaluated the performance of two different commercial platforms on red blood cell-depleted whole blood cells: 10x Genomics Flex v1 and Honeycomb HIVE v1.These data are publicly available from the Gene Expression Omnibus database (accession number GSE266615).Further insights could be gained by correcting batch and technical effects introduced by storage time after fixation and cell numbers fixed. These data may be used to examine how reflective the transcriptome of neutrophils are of the native environment.http://www.sciencedirect.com/science/article/pii/S235234092401058810x genomics flexPreservationNeutrophilsTranscriptome |
| spellingShingle | Daniel V Brown Agnieszka Swierczak Yue You Yupei You Daniela Amann-Zalcenstein Peter Hickey Arthur Hsu Matthew E. Ritchie Monther Alhamdoosh Judith Field Rory Bowden A dataset examining technical factors on fixed white blood cell single-cell RNA-seqGene expression Omnibus Data in Brief 10x genomics flex Preservation Neutrophils Transcriptome |
| title | A dataset examining technical factors on fixed white blood cell single-cell RNA-seqGene expression Omnibus |
| title_full | A dataset examining technical factors on fixed white blood cell single-cell RNA-seqGene expression Omnibus |
| title_fullStr | A dataset examining technical factors on fixed white blood cell single-cell RNA-seqGene expression Omnibus |
| title_full_unstemmed | A dataset examining technical factors on fixed white blood cell single-cell RNA-seqGene expression Omnibus |
| title_short | A dataset examining technical factors on fixed white blood cell single-cell RNA-seqGene expression Omnibus |
| title_sort | dataset examining technical factors on fixed white blood cell single cell rna seqgene expression omnibus |
| topic | 10x genomics flex Preservation Neutrophils Transcriptome |
| url | http://www.sciencedirect.com/science/article/pii/S2352340924010588 |
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