PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments

Hershberg, Elliot A.; Camplisson, Conor K.; Close, Jennie; Attar, Sahar; Chern, Ryan; Liu, Yuzhen; Akilesh, Shreeram; Nicovich, Philip R.; Beliveau, Brian J.

doi:10.1038/s41592-021-01187-3

Cited by 24 publications

(27 citation statements)

References 65 publications

(107 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To test the applicability of pSABER to more challenging DNA ISH applications, we performed experiments targeting the human alpha satellite repeat DNA region in K29Mes cells (Fig. 2b) as well as a 200 kb single-copy chromosomal region on Xp22.32 (hg38 chrX:5400000–5600000) using a previously validated complex oligo library and an accompanying readout probe 31 on primary human metaphase chromosome spreads (Fig. 2c).…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Programmable peroxidase-assisted signal amplification enables flexible detection of nucleic acid targets in cellular and histopathological specimens

Attar

Browning

Liu

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

In situ hybridization (ISH) is a powerful tool for investigating the spatial arrangement of nucleic acid targets in fixed samples. ISH is typically visualized using fluorophores to allow high sensitivity and multiplexing or with colorimetric labels to facilitate co-visualization with histopathological stains. Both approaches benefit from signal amplification, which makes target detection effective, rapid, and compatible with a broad range of optical systems. Here, we introduce a unified technical platform, termed "pSABER", for the amplification of ISH signals in cell and tissue systems. pSABER decorates the in situ target with concatemeric binding sites for a horseradish peroxidase-conjugated oligonucleotide which can then catalyze the massive localized deposition of fluorescent or colorimetric substrates. We demonstrate that pSABER effectively labels DNA and RNA targets, works robustly in cultured cells and challenging formalin fixed paraffin embedded (FFPE) specimens. Furthermore, pSABER can achieve 25-fold signal amplification over conventional signal amplification by exchange reaction (SABER) and can be serially multiplexed using solution exchange. Therefore, by linking nucleic acid detection to robust signal amplification capable of diverse readouts, pSABER will have broad utility in research and clinical settings.

show abstract

Section: Resultsmentioning

confidence: 99%

“…The complex oligo library used to target Xp22.32 was purchased from Twist Biosciences and amplified and processed as described previously 31 . The sequences of the oligos probes used are listed in Supplementary Dataset 1.…”

Section: Fish Probesmentioning

confidence: 99%

Programmable peroxidase-assisted signal amplification enables flexible detection of nucleic acid targets in cellular and histopathological specimens

Attar

Browning

Liu

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…FISH validations were done on four new sections from a mouse littermate of the source animal used for Light-Seq experiments. SABER-FISH probes were designed using the ‘RNA Probe Design’ feature of the PaintSHOP tool ( https://oligo.shinyapps.io/paintshop/ ) 77 . For each gene, all probes were appended with a common gene-specific SABER-FISH primer sequence for orthogonal detection of multiple genes in the same cells.…”

Section: Methodsmentioning

confidence: 99%

Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing

et al. 2022

View full text Add to dashboard Cite

We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding in fixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially targeted, rapid photocrosslinking of DNA barcodes onto complementary DNAs in situ with a one-step DNA stitching reaction to create pooled, spatially indexed sequencing libraries. This light-directed barcoding enables in situ selection of multiple cell populations in intact fixed tissue samples for full-transcriptome sequencing based on location, morphology or protein stains, without cellular dissociation. Applying Light-Seq to mouse retinal sections, we recovered thousands of differentially enriched transcripts from three cellular layers and discovered biomarkers for a very rare neuronal subtype, dopaminergic amacrine cells, from only four to eight individual cells per section. Light-Seq provides an accessible workflow to combine in situ imaging and protein staining with next generation sequencing of the same cells, leaving the sample intact for further analysis post-sequencing.

show abstract

“…Oligo pools were generated using the PaintSHOP application ( Hershberg et al, 2021 ) from the Drosophila dm6 reference genome. A complete list of oligos can be found in Data S1 , Table S2 .…”

Section: Methodsmentioning

confidence: 99%

Nucleoporins facilitate ORC loading onto chromatin

Richards¹,

Lord²,

Benton³

et al. 2022

Cell Reports

View full text Add to dashboard Cite

PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments

Cited by 24 publications

References 65 publications

Programmable peroxidase-assisted signal amplification enables flexible detection of nucleic acid targets in cellular and histopathological specimens

Programmable peroxidase-assisted signal amplification enables flexible detection of nucleic acid targets in cellular and histopathological specimens

Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing

Nucleoporins facilitate ORC loading onto chromatin

Contact Info

Product

Resources

About