Journal: Scientific Reports

Article Title: Aging and putative frailty biomarkers are altered by spaceflight

doi: 10.1038/s41598-024-57948-5

Figure Lengend Snippet: Genelab datasets analyzed in the manuscript.

Article Snippet: OSD-99 , Rodent Research-1 (RR1) NASA Validation Flight: Mouse extensor digitorum longus muscle transcriptomic and epigenomic data , Galazka J, Globus R "Rodent Research 1", GeneLab, Version 4, http://doi.org/10.26030/1h3m-3q49 , Extensor digitorum longus muscle.

Techniques: Gene Expression, Expressing, Biomarker Discovery, Irradiation

Journal: Scientific Reports

Article Title: High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution

doi: 10.1038/s41598-024-82736-6

Figure Lengend Snippet: TempO-LINC workflow and study overview. ( a ) The TempO-LINC workflow begins with fixation of cells or nuclei and subsequent storage at −80 o C. Fixed cells are thawed and hybridized with Detector Oligo (DO) probe pools that are then ligated. Split pool barcoding with three rounds of ligation is then performed. Following ligation of barcodes, cells are pooled again and redistributed into a final 96-well plate where sequencing adaptors and index sequences are added during PCR amplification. Amplified libraries are then purified and sequenced. Data analysis begins with demultiplexing to associate gene expression profiles with cell-identifying barcodes. ( b ) Schematic of TempO-LINC 310 bp library structure including the three barcodes that are ligated as well as the i5 and i7 index positions that serve as a fourth barcode to identify cells. The table shows total barcode diversity created through each round of barcoding as well as the molecular mechanism for barcoding. ( c ) Overview of TempO-LINC validation experiments performed for this study. Experiments were a combination of gene expression profiling on mixtures of multiple human and mouse cell lines as well as nuclei isolated from adult mouse brain, lung and kidney tissue.

Article Snippet: HEK293T cells were incubated with 45 µL of a Human Whole Transcriptome v2.1 (22,533 probe pairs, BioSpyder, cat #201828) detector oligo (DO) pool, and NIH3T3 cells were incubated with 45 µL of a Mouse Whole Transcriptome v1.1 (30,146 probe pairs, BioSpyder, cat# 201186) DO pool overnight for 16 h at 45 o C. Following hybridization, cells were centrifuged for 5 min at 500 rcf and were washed twice with 750 µL of 1X Ligation buffer.

Techniques: Ligation, Sequencing, Amplification, Purification, Expressing, Isolation

Journal: Scientific Reports

Article Title: High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution

doi: 10.1038/s41598-024-82736-6

Figure Lengend Snippet: TempO-LINC workflow and study overview. ( a ) The TempO-LINC workflow begins with fixation of cells or nuclei and subsequent storage at −80 o C. Fixed cells are thawed and hybridized with Detector Oligo (DO) probe pools that are then ligated. Split pool barcoding with three rounds of ligation is then performed. Following ligation of barcodes, cells are pooled again and redistributed into a final 96-well plate where sequencing adaptors and index sequences are added during PCR amplification. Amplified libraries are then purified and sequenced. Data analysis begins with demultiplexing to associate gene expression profiles with cell-identifying barcodes. ( b ) Schematic of TempO-LINC 310 bp library structure including the three barcodes that are ligated as well as the i5 and i7 index positions that serve as a fourth barcode to identify cells. The table shows total barcode diversity created through each round of barcoding as well as the molecular mechanism for barcoding. ( c ) Overview of TempO-LINC validation experiments performed for this study. Experiments were a combination of gene expression profiling on mixtures of multiple human and mouse cell lines as well as nuclei isolated from adult mouse brain, lung and kidney tissue.

Article Snippet: Nuclei were resuspended in 55 μL TempO-LINC 1X Hybridization buffer and 45 μL of a Mouse Whole Transcriptome v1.1 (30,162 probe pairs, BioSpyder, cat# 201186) DO pool and placed in an incubator overnight for 16 h at 45 o C. Next, 100,000 nuclei were transferred and prepped for TempO-LINC Barcoding.

Techniques: Ligation, Sequencing, Amplification, Purification, Gene Expression, Biomarker Discovery, Isolation