A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencing

Ernst Lengyel, Yan Li, Melanie Weigert, Lisha Zhu, Heather Eckart, Melissa Javellana, Sarah Ackroyd, Jason Xiao, Susan Olalekan, Dianne Glass, Shilpa Iyer, Rahul Krishnan, Agnes Julia Bilecz, Ricardo Lastra, Mengjie Chen, Anindita Basu

Abstract

As part of the Human Cell Atlas Initiative, our goal is to generate single-cell transcriptomics (single-cell RNA sequencing [scRNA-seq], 86,708 cells) and regulatory (single-cell assay on transposase accessible chromatin sequencing [scATAC-seq], 59,830 cells) profiles of the normal postmenopausal ovary and fallopian tube (FT). The FT contains 11 major cell types, and the ovary contains 6. The dominating cell type in the FT and ovary is the stromal cell, which expresses aging-associated genes. FT epithelial cells express multiple ovarian cancer risk-associated genes (CCDC170, RND3, TACC2, STK33, and ADGB) and show active communication between fimbrial epithelial cells and ovarian stromal cells. Integrated single-cell transcriptomics and chromatin accessibility data show that the regulatory landscape of the fimbriae is different from other anatomic regions. Cell types with similar gene expression in the FT display transcriptional profiles. These findings allow us to disentangle the cellular makeup of the postmenopausal FT and ovary, advancing our knowledge of gynecologic diseases in menopause.

Datasets

1. Fallopian tube RNA
Metadata
donor_id
self_reported_ethnicity_ontology_term_id
organism_ontology_term_id
sample_uuid
sample_preservation_method
tissue_ontology_term_id
development_stage_ontology_term_id
suspension_uuid
suspension_type
library_uuid
assay_ontology_term_id
mapped_reference_annotation
cell_type_ontology_term_id
author_cell_type
disease_ontology_term_id
sex_ontology_term_id
expCond
tissue_type
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
D5_329616964 cells
D3_320314386 cells
D6_336912402 cells
D4_32957755 cells
D7_33915675 cells
D2_30611872 cells
D1_30411520 cells
Preview
A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencing
2. Ovary RNA
Metadata
donor_id
self_reported_ethnicity_ontology_term_id
organism_ontology_term_id
sample_uuid
sample_preservation_method
tissue_ontology_term_id
development_stage_ontology_term_id
suspension_uuid
suspension_type
library_uuid
assay_ontology_term_id
mapped_reference_annotation
cell_type_ontology_term_id
author_cell_type
disease_ontology_term_id
sex_ontology_term_id
expCond
tissue_type
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
D3_32037178 cells
D8_34535798 cells
D5_32964931 cells
D7_33914425 cells
D2_30612118 cells
D1_30411684 cells
Preview
A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencing

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Dataset 1
Dataset 2
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Source data

https://cellxgene.cziscience.com/collections/d36ca85c-3e8b-444c-ba3e-a645040c6185

Alias names

EGAS00001006780

Cite this study

Lengyel, E., Li, Y., Weigert, M., Zhu, L., Eckart, H., Javellana, M., Ackroyd, S., Xiao, J., Olalekan, S., Glass, D. and Iyer, S., 2022. A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencing. Cell Reports, 41(12). https://doi.org/10.1016/j.celrep.2022.111838