Single Nucleus Pituitary Atlas


Notice: This web app is under active development at the moment. You may encounter disruption of usage and incomplete features.

Data Browser

Browse the expression, chromatin accessibility and methylation profile of your gene of interest, either at single cell level or cell type level.

Inferred cis-Regulatory Regions

Browse the potential cis-regulatory regions of your gene of interest. The cis-regulatory regions were inferred from co-accessibility between distal elements and promoters, calculated using the CICERO package.

Regulons

Browse the regulons (TF and its potential target genes) reconstructed from the snRNAseq data. The regulons were reconstructed using the SCENIC pipeline.



Data Browser

Coembed shows the UMAP overlay of all the cells from all selected samples and assays. Note that currently the single nucleus methylation data is only available for mouse and is pooled from 30 male animals.
Gene browser shows the RNA expression, chromatin accessibility (ATAC) and methylation profiles of your choice of gene. It shows the gene at single-cell resolution in the same UMAP plot. It also shows at cell-type resolution in the format of violin plot for gene expression and bigWig tracks for chromatin accessibility and methylation profiles. Note that currently the methylation profile is only available for mouse.

Coembed

Choose the animals and data assays to show in the UMAP coembed plot. Choose to color the cells by assay, animal or cell type.

Gene Browser

Choose a gene to show it's expression, chromatin accessibility and methylation profiles. Note that methylation is only available for mouse.
Note that the animal / subject is chosen for RNA and ATAC, Methylation data is pooled from 30 male mice.

Coembed

Single Cell Gene Browser

RNA

ATAC

Methylation

Cell Type Gene Expression

Cell Type ATAC and Methylation


Inferred cis-Regulatory Regions

Browse the potential cis-regulatory regions of your gene of interest. The cis-regulatory regions were inferred from co-accessibility between distal elements and promoters, calculated using the CICERO package.

Gene

Choose a gene to show its putative regulatory regions

Gene-centered Putative Regulatary Regions

Regulons analysis

A regulon is defined as a set of genes including one transcription factor (TF) and all its potential target genes. The regulons were reconstructed using the SCENIC pipeline. You can select a regulon (represented by the name of the TF) to explore its enrichment in individual cells or cell types.

Regulon

Choose a regulon (TF name) to show its information

Top regulons in each cell type

Regulon activity at single-cell resolution

Regulon info


Regulon

Choose a regulon (TF name) to show its information

Regulon activity at cell-type resolution


Introduction

Cite

Single nucleus multi-omics regulatory atlas of the murine pituitary
Frederique Ruf-Zamojski, Zidong Zhang, Michel Zamojski, Gregory R. Smith, Natalia Mendelev, Hanqing Liu, German Nudelman, Mika Moriwaki, Hanna Pincas, Rosa Gomez Castanon, Venugopalan D. Nair, Nitish Seenarine, Mary Anne S. Amper, Xiang Zhou, Luisina Ongaro, Chirine Toufaily, Gauthier Schang, Joseph R. Nery, Anna Bartlett, Andrew Aldridge, Nimisha Jain, Gwen V. Childs, Olga G. Troyanskaya, Joseph R. Ecker, Judith L. Turgeon, Corrine K. Welt, Daniel J. Bernard, Stuart C. Sealfon
bioRxiv 2020.06.06.138024; doi: https://doi.org/10.1101/2020.06.06.138024

Single nucleus pituitary transcriptomic and epigenetic landscape reveals human stem cell heterogeneity with diverse regulatory mechanisms
Zidong Zhang, Michel Zamojski, Gregory R. Smith, Thea L. Willis, Val Yianni, Natalia Mendelev, Hanna Pincas, Nitish Seenarine, Mary Anne S. Amper, Mital Vasoya, Venugopalan D. Nair, Judith L. Turgeon, Daniel J. Bernard, Olga G. Troyanskaya, Cynthia L. Andoniadou, Stuart C. Sealfon, Frederique Ruf-Zamojski
bioRxiv 2021.06.18.449034; doi: https://doi.org/10.1101/2021.06.18.449034

Funding

This work was supported by funding from the National Institute of Health (NIH) Grant DK46943 (SCS), the Canadian Institutes of Health Research (CIHR) Project Grants PJT-162343 (DJB) and PJT-169184 (DJB), NIH award R01HD065029 from the Eunice Kennedy Shriver National Institute Of Child Health & Human Development (CKW), NIH NICHD R01HD093461 (GVC), NIH R01HD087057 (GVC), and NIH NIDDK 1R01DK113776-01 (GVC).