CryoGrid-PIXUL-RNA: high throughput RNA isolation platform for tissue transcript analysis
Abstract Background Disease molecular complexity requires high throughput workflows to map disease pathways through analysis of vast tissue repositories. Great progress has been made in tissue multiomics analytical technologies. To match the high throughput of these advanced analytical platforms, we...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-08-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-023-09527-7 |
| _version_ | 1797453769600925696 |
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| author | Scott A. Schactler Stephen J. Scheuerman Andrea Lius William A. Altemeier Dowon An Thomas J. Matula Michal Mikula Maria Kulecka Oleg Denisenko Daniel Mar Karol Bomsztyk |
| author_facet | Scott A. Schactler Stephen J. Scheuerman Andrea Lius William A. Altemeier Dowon An Thomas J. Matula Michal Mikula Maria Kulecka Oleg Denisenko Daniel Mar Karol Bomsztyk |
| author_sort | Scott A. Schactler |
| collection | DOAJ |
| description | Abstract Background Disease molecular complexity requires high throughput workflows to map disease pathways through analysis of vast tissue repositories. Great progress has been made in tissue multiomics analytical technologies. To match the high throughput of these advanced analytical platforms, we have previously developed a multipurpose 96-well microplate sonicator, PIXUL, that can be used in multiple workflows to extract analytes from cultured cells and tissue fragments for various downstream molecular assays. And yet, the sample preparation devices, such as PIXUL, along with the downstream multiomics analytical capabilities have not been fully exploited to interrogate tissues because storing and sampling of such biospecimens remain, in comparison, inefficient. Results To mitigate this tissue interrogation bottleneck, we have developed a low-cost user-friendly system, CryoGrid, to catalog, cryostore and sample tissue fragments. TRIzol is widely used to isolate RNA but it is labor-intensive, hazardous, requires fume-hoods, and is an expensive reagent. Columns are also commonly used to extract RNA but they involve many steps, are prone to human errors, and are also expensive. Both TRIzol and column protocols use test tubes. We developed a microplate PIXUL-based TRIzol-free and column-free RNA isolation protocol that uses a buffer containing proteinase K (PK buffer). We have integrated the CryoGrid system with PIXUL-based PK buffer, TRIzol, and PureLink column methods to isolate RNA for gene-specific qPCR and genome-wide transcript analyses. CryoGrid-PIXUL, when integrated with either PK buffer, TRIzol or PureLink column RNA isolation protocols, yielded similar transcript profiles in frozen organs (brain, heart, kidney and liver) from a mouse model of sepsis. Conclusions RNA isolation using the CryoGrid-PIXUL system combined with the 96-well microplate PK buffer method offers an inexpensive user-friendly high throughput workflow to study transcriptional responses in tissues in health and disease as well as in therapeutic interventions. |
| first_indexed | 2024-03-09T15:27:39Z |
| format | Article |
| id | doaj.art-cd39d825b9a040c79fcfc18106dd7838 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-09T15:27:39Z |
| publishDate | 2023-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-cd39d825b9a040c79fcfc18106dd78382023-11-26T12:26:08ZengBMCBMC Genomics1471-21642023-08-0124111610.1186/s12864-023-09527-7CryoGrid-PIXUL-RNA: high throughput RNA isolation platform for tissue transcript analysisScott A. Schactler0Stephen J. Scheuerman1Andrea Lius2William A. Altemeier3Dowon An4Thomas J. Matula5Michal Mikula6Maria Kulecka7Oleg Denisenko8Daniel Mar9Karol Bomsztyk10UW Medicine South Lake Union, University of WashingtonUW Medicine South Lake Union, University of WashingtonUW Medicine South Lake Union, University of WashingtonUW Medicine South Lake Union, University of WashingtonUW Medicine South Lake Union, University of WashingtonCenter for Industrial and Medical Ultrasound, Applied Physics Laboratory, University of WashingtonDepartment of Genetics, Maria Sklodowska-Curie National Research Institute of OncologyDepartment of Genetics, Maria Sklodowska-Curie National Research Institute of OncologyUW Medicine South Lake Union, University of WashingtonUW Medicine South Lake Union, University of WashingtonUW Medicine South Lake Union, University of WashingtonAbstract Background Disease molecular complexity requires high throughput workflows to map disease pathways through analysis of vast tissue repositories. Great progress has been made in tissue multiomics analytical technologies. To match the high throughput of these advanced analytical platforms, we have previously developed a multipurpose 96-well microplate sonicator, PIXUL, that can be used in multiple workflows to extract analytes from cultured cells and tissue fragments for various downstream molecular assays. And yet, the sample preparation devices, such as PIXUL, along with the downstream multiomics analytical capabilities have not been fully exploited to interrogate tissues because storing and sampling of such biospecimens remain, in comparison, inefficient. Results To mitigate this tissue interrogation bottleneck, we have developed a low-cost user-friendly system, CryoGrid, to catalog, cryostore and sample tissue fragments. TRIzol is widely used to isolate RNA but it is labor-intensive, hazardous, requires fume-hoods, and is an expensive reagent. Columns are also commonly used to extract RNA but they involve many steps, are prone to human errors, and are also expensive. Both TRIzol and column protocols use test tubes. We developed a microplate PIXUL-based TRIzol-free and column-free RNA isolation protocol that uses a buffer containing proteinase K (PK buffer). We have integrated the CryoGrid system with PIXUL-based PK buffer, TRIzol, and PureLink column methods to isolate RNA for gene-specific qPCR and genome-wide transcript analyses. CryoGrid-PIXUL, when integrated with either PK buffer, TRIzol or PureLink column RNA isolation protocols, yielded similar transcript profiles in frozen organs (brain, heart, kidney and liver) from a mouse model of sepsis. Conclusions RNA isolation using the CryoGrid-PIXUL system combined with the 96-well microplate PK buffer method offers an inexpensive user-friendly high throughput workflow to study transcriptional responses in tissues in health and disease as well as in therapeutic interventions.https://doi.org/10.1186/s12864-023-09527-7CryoGrid for tissues cryostoring and samplingProteinase KPIXUL RNA extractionRNA sequencingTranscriptomics |
| spellingShingle | Scott A. Schactler Stephen J. Scheuerman Andrea Lius William A. Altemeier Dowon An Thomas J. Matula Michal Mikula Maria Kulecka Oleg Denisenko Daniel Mar Karol Bomsztyk CryoGrid-PIXUL-RNA: high throughput RNA isolation platform for tissue transcript analysis BMC Genomics CryoGrid for tissues cryostoring and sampling Proteinase K PIXUL RNA extraction RNA sequencing Transcriptomics |
| title | CryoGrid-PIXUL-RNA: high throughput RNA isolation platform for tissue transcript analysis |
| title_full | CryoGrid-PIXUL-RNA: high throughput RNA isolation platform for tissue transcript analysis |
| title_fullStr | CryoGrid-PIXUL-RNA: high throughput RNA isolation platform for tissue transcript analysis |
| title_full_unstemmed | CryoGrid-PIXUL-RNA: high throughput RNA isolation platform for tissue transcript analysis |
| title_short | CryoGrid-PIXUL-RNA: high throughput RNA isolation platform for tissue transcript analysis |
| title_sort | cryogrid pixul rna high throughput rna isolation platform for tissue transcript analysis |
| topic | CryoGrid for tissues cryostoring and sampling Proteinase K PIXUL RNA extraction RNA sequencing Transcriptomics |
| url | https://doi.org/10.1186/s12864-023-09527-7 |
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