# Patch-seq Method

**URL:** <https://community.brain-map.org/t/patch-seq-method/2700>\
**Category:** How To\
**Tags:** transcriptomics, electrophysiology, single-cell-morphology\
**Created:** [November 9, 2023, 12:25am UTC](https://community.brain-map.org/t/patch-seq-method/2700 "2023-11-09T00:25:37Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![racheld](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/racheld/32/107_2.png) [@racheld](https://community.brain-map.org/u/racheld)\
**Post date:** [November 9, 2023, 12:25am UTC](https://community.brain-map.org/t/patch-seq-method/2700/1 "2023-11-09T00:25:38Z")

</div>

# Patch-seq Method

The method in which the morphology, electrophysiology and transcriptome (gene expression) profiles are assayed simultaneously from the same neuron. Here we detail the various steps and tools to generate data across species and brain regions.

- Slice Preparation and Blockface Imaging

- [Patch-seq Electrophysiology Protocol](https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-5qpvoyb2bg4o/v2)

- [SMARTerSC Amplification for single-cell or single-nuclei RNASeq](https://www.protocols.io/view/smarterv4-1x-amplification-for-single-cell-or-sing-261geopdjl47/v2)

- [Post Patch Clamp Slice Fixation](https://www.protocols.io/view/post-patch-clamp-slice-fixation-bp2l6n8qrgqe/v5)

- [Gelatin Coated Slides](https://www.protocols.io/view/coating-slides-with-gelatin-e6nvw9qm2gmk/v2)

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# Imaging

- [20X Imaging Protocol](https://www.protocols.io/view/zeiss-axioimager-multi-channel-20x-image-capture-bp2l6n85rgqe/v2)
- [63X Imaging Protocol](http://dx.doi.org/10.17504/protocols.io.bdpmi5k6)

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# Morphology Reconstruction

- [Reconstruction tool kit](https://portal.brain-map.org/explore/toolkit/morpho-reconstruction/vaa3d-mozak)
- [Reconstruction Protocol](https://www.protocols.io/view/3d-reconstruction-of-neurons-in-vaa3d-v-3-36wgq5683gk5/v3)
- [Morphology Analysis tool: Skeleton Keys](https://skeleton-keys.readthedocs.io/en/latest/guide.html)

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# Questions?

Refer to our Patch-seq methods paper: [Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization | eLife](https://doi.org/10.7554/elife.65482)

Or post a question to the [Community Forum](https://community.brain-map.org/) using any of the relevant tags below:  
[analysis](https://community.brain-map.org/tag/analysis), [celltype](https://community.brain-map.org/tag/celltype), [electrophysiology](https://community.brain-map.org/tag/electrophysiology), [experiment-design](https://community.brain-map.org/tag/experiment-design), [histology](https://community.brain-map.org/tag/histology), [how-to](https://community.brain-map.org/tag/how-to), [single-cell-morphology](https://community.brain-map.org/tag/single-cell-morphology), [transcriptomics](https://community.brain-map.org/tag/transcriptomics)