Journal: Communications Biology

Article Title: The spatial RNA integrity number assay for in situ evaluation of transcriptome quality

doi: 10.1038/s42003-020-01573-1

Figure Lengend Snippet: a Schematics of an one cell layer thick tissue section placed on a pre-printed fully coated capture area for 18S rRNA, leading to the formation of a c18RNA-footprint. b Schematic depiction of the sequential probe hybridization. c Total RNA gel electropherogram of a mouse olfactory bulb tissue sample together with d a heat map visualization of the section’s spatial RNA integrity number (sRIN) distribution based on its c18RNA footprint ( n = 4, technical replicates) and e a HE image of the same section (scale bar: 600 µm), boxes enclose regions shown in close-up. f Close-up of HE image (scale bar: 200 µm) and g sRIN heat map, arrows marks cells from different areas in the tissue with high sRIN values, the left box depicts a group of cells where cell drop-out has occurred compared to the right box that depicts a group of cells recording high sRIN values.

Article Snippet: The script for generating sRIN heat maps from tif files in RStudio, can be found at https://github.com/ludvigla/sRIN and on Mendeley .

Techniques: Hybridization

Journal: Communications Biology

Article Title: The spatial RNA integrity number assay for in situ evaluation of transcriptome quality

doi: 10.1038/s42003-020-01573-1

Figure Lengend Snippet: a HE image (scale bar: 600 µm) and b sRIN heat map of the same mouse olfactory bulb displayed in Fig. , generated from a freshly frozen tissue section after brief formalin (10%) fixation to simulate fragmentation by cross-linking ( n = 4, technical replicates).

Article Snippet: The script for generating sRIN heat maps from tif files in RStudio, can be found at https://github.com/ludvigla/sRIN and on Mendeley .

Techniques: Generated

Journal: Communications Biology

Article Title: The spatial RNA integrity number assay for in situ evaluation of transcriptome quality

doi: 10.1038/s42003-020-01573-1

Figure Lengend Snippet: a – l Luminal B breast tumor tissue sections from two patients ( n = 3, technical replicates each). a HE image (scale bar: 1 mm) and b sRIN heat map, boxes enclose regions shown in close-up. Close-up of c HE image (scale bar: 200 µm) and d sRIN heat map. e HE image (scale bar: 1 mm) and f sRIN heat map, boxes enclose regions shown in close-up. Close-up of g HE image (scale bar: 150 µm) and h sRIN heat map. Close-up of i HE image (scale bar: 200 µm) and j sRIN heat map. Close-up of k HE image (scale bar: 100 µm) and l sRIN heat map, arrows show areas of very high (10) sRIN values and varied cell density. m HE image (scale bar: 80 µm) and n sRIN heat map of a gray matter region from a post-mortem brain ( n = 3, biological replicates).

Article Snippet: The script for generating sRIN heat maps from tif files in RStudio, can be found at https://github.com/ludvigla/sRIN and on Mendeley .

Techniques:

Journal: Communications Biology

Article Title: The spatial RNA integrity number assay for in situ evaluation of transcriptome quality

doi: 10.1038/s42003-020-01573-1

Figure Lengend Snippet: a HE image (scale bar: 1 mm) and b sRIN heat map of a malignant childhood brain tumor diagnosed as anaplastic medulloblastoma grade IV ( n = 4, technical replicates), boxes enclose regions shown in close-up. c HE image (scale bar: 1 mm) and d ST analysis showing unique genes, of the same childhood brain tumor ( n = 2, technical replicates). Close-up of e HE (scale bar: 200 µm) image and f sRIN heat map of the same childhood brain tumor where deep blue areas represent intact cell rich tumor and in light purple areas the tumor is necrotic. The sRIN heat map show areas of varied sRIN values in the tumor areas and no sRIN values in necrotic areas, boxes enclose regions shown in close-up. Close-up of g HE (scale bar: 40 µm) image and h sRIN heat map of the same childhood brain tumor show areas of similar HE staining pattern and varied sRIN values.

Article Snippet: The script for generating sRIN heat maps from tif files in RStudio, can be found at https://github.com/ludvigla/sRIN and on Mendeley .

Techniques: Staining