Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing

Bin Yang, Jennifer B. Treweek, Rajan P. Kulkarni, +6

Cell

MedicineHuman TissueTissue PhysiologyTransparent Intact TissueBiomedical Engineering +3

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

Sheel Shah, Eric Lubeck, Wen Zhou, +1

Neuron

Cell LineageEngineeringSingle Cell SequencingMedicineSingle-cell Genomics +8

Integrated spatial genomics reveals global architecture of single nuclei

Yodai Takei, Jina Yun, Shiwei Zheng, +10

Nature

Functional GenomicsEngineeringSingle Cell SequencingMedicineGenetics +8

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

Sheel Shah, Yodai Takei, Wen Zhou, +9

Cell

BiologyDevelopmental BiologyIntron SeqfishSequence AnalysisComputational Biology +8

Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data

Qian Zhu, Sheel Shah, Ruben Dries, +2

Nature Biotechnology

BiologyGenetic DiversityHybridisationMedicineGenetics +9

Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior

Dong‐Wook Kim, Zizhen Yao, Lucas T. Graybuck, +16

Cell

Brain MechanismAffective NeuroscienceSocial SciencesSocial NeuroscienceCell Types +14

Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing

Sheel Shah, Eric Lubeck, Maayan Schwarzkopf, +8

Development

EngineeringSingle-molecule Rna DetectionMolecular BiologyBiomedical EngineeringRobust Detection +20

seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus

Sheel Shah, Eric Lubeck, Wen Zhou, +1

Neuron

Molecular NeuroscienceDevelopmental BiologyBrain CircuitryBrain MechanismNeuroanatomy +7

Single-cell nuclear architecture across cell types in the mouse brain

Yodai Takei, Shiwei Zheng, Jina Yun, +7

Science

Nuclear StructureEpigenetic ChangeNuclear ArchitecturesSpatial OmicsCellular Neurobiology +22

Profiling the transcriptome with RNA SPOTs

Chee-Huat Linus Eng, Sheel Shah, Julian Thomassie, +1

Nature Methods

BioinformaticsSystems BiologyGene Sequence AnnotationGeneticsTranscriptomics Technology +6