Transcriptomics

Dataset Information

299

Expression profiles of cultured human epididymis cells reveal the functional diversity of caput, corpus and cauda regions.


ABSTRACT: Purpose: To compare the transcriptome profiles (RNA-seq) of cultured human epididymis cells and tissue from the caput, corpus and cauda regions of the human epididymis. Methods: Human epididymis tissue was obtained with Institutional Review Board approval from 3 patients (UC05, UC06, UC09, range: 22 - 36 years) undergoing inguinal radical orchiectomy for a clinical diagnosis of testicular cancer. None of the epididymides had extension of the testicular cancer. The three anatomical regions: caput, corpus and cauda, were separated and segments of each snap frozen. Adult human epididymis epithelial (HEE) cultures were also established from tissue. RNA was extracted from both tissue and cultured HEE cells and RNA-seq libraries prepared (TruSeq RNA Sample Preparation Kit v2, Low-Throughput protocol, Illumina). Libraries were sequenced on Illumina HiSeq2500 machines. Data were analyzed using TopHat and Cufflinks. Results: Libraries generated ~19-39 million reads per library from the cells (95-99% mapping to the human genome) and ~14-39 million reads from the tissue samples (84-99% mapped). Raw reads were aligned to the genome with Tophat and gene expression values were processed using Cufflinks as Fragments Per Kilobase per Million mapped fragments (FPKM). FPKM values were subject to principle component analysis, which revealed that though caput, corpus and cauda cell samples respectively from UC05, UC06 and UC09 clustered together. RNA-seq data from the 3 biological replicas (UC05, UC06 and UC09) of caput, corpus and cauda were pooled for further analysis. Cufflinks was used to determine differentially expressed genes (DEGs) between caput, corpus and cauda cells, combined from the 3 donors. The gene expression profiles of corpus and cauda are remarkably similar and both differ from the caput to a similar degree. We identified ~40 genes differentially expressed between corpus and cauda and more than 1600 DEGs between caput and cauda. The DEGs for each comparison (caput and corpus/cauda) were analysed using a gene ontology process enrichment analysis (DAVID, Huang et al., NAR 2009;37:1-13, Huang et al., 2009 Nat Prot 4:44-57). Conclusions: Here we describe an in depth analysis of the gene expression repertoire of primary cultures of epithelial cells and intact tissues from each region of the adult human epididymis. These data will be valuable to decipher pathways of normal epididymis function and aspects of epididymis disease that cause male infertility. RNA-seq was performed on libraries generated from caput, corpus and cauda-derived cultured cells (passage 2 or 3) from 3 donors and on caput, corpus and cauda tissue from 2 of the same donors. Donor age range: 22 - 36 years.

ORGANISM(S): Homo sapiens  

SUBMITTER: James Browne   Rui Yang  Ann Harris 

PROVIDER: E-GEOD-72986 | ArrayExpress | 2016-01-04

SECONDARY ACCESSION(S): GSE72986SRP063661PRJNA295529

REPOSITORIES: GEO, ArrayExpress, ENA

altmetric image

Publications

Expression profiles of human epididymis epithelial cells reveal the functional diversity of caput, corpus and cauda regions.

Browne James A JA   Yang Rui R   Leir Shih-Hsing SH   Eggener Scott E SE   Harris Ann A  

Molecular human reproduction 20151126 2


Region-specific transcriptional profiling of tissues and cultured epithelial cells from the human epididymis will predict functional specialization along the duct.We identified the molecular signature driving functions of the caput, corpus and cauda epithelium, and determined how these differ to establish the regional differentiation of the organ.The epithelium lining the human male genital ducts has a critical role in fertility. In particular, it controls the luminal environment in the epididym  ...[more]

Similar Datasets

2007-09-25 | GSE7808 | GEO
2010-08-26 | GSE23812 | GEO
2008-06-15 | E-GEOD-7808 | ArrayExpress
2010-08-25 | E-GEOD-23812 | ArrayExpress
| GSE77139 | GEO
| GSE96602 | GEO
| GSE76377 | GEO
2012-06-30 | E-GEOD-35522 | ArrayExpress
| GSE76376 | GEO
| GSE44365 | GEO