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Series GSE60381 Query DataSets for GSE60381
Status Public on Jan 07, 2015
Title Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function [Agilent expression]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The epithelium lining the epididymis in the male reproductive tract maintains a luminal environment that promotes sperm cell maturation. This process is dependent on the coordinated expression of many genes that encode proteins with a role in epithelial transport. We previously generated genome-wide maps of open chromatin in primary human fetal epididymis epithelial cells to identify potential regulatory elements controlling coordinated gene expression in the epididymis epithelium. Subsequent in silico analysis identified transcription factor binding sites (TFBS) that were over-represented in the HEE open chromatin, include the motif for paired box 2 (PAX2). PAX2 is a critical transcriptional regulator of urogenital tract development, which is well studied in the kidney but is unexplored in the epididymis. Due to the limited lifespan of primary HEE cells in culture we investigated the role of PAX2 in an immortalized HEE cell line (REP). First, REP cells were evaluated by DNase-seq and their open chromatin map overlapped that of primary HEE cells at ~ 65% of sites. Moreover, the PAX2-binding motif was again identified as an overrepresented TFBS within intergenic open chromatin, though on fewer chromosomes than in the primary HEE cells. To identify PAX2-target genes in REP cells, RNA-seq analysis was performed after siRNA-mediated depletion of PAX2 in comparison to a non-targeting siRNA. In response to PAX2-represssion, 3142 transcripts were differentially expressed (1334 up-regulated and 1808 down-regulated). Novel PAX2 targets included multiple genes encoding proteins with a predicted function in the epididymis epithelium.
Overall design Gene expression in REP cells was measured at 16 hours after exposure to 1nM R1881 or vehicle control.
Contributor(s) Browne J, Yang R
Citation(s) 25180270
Submission date Aug 13, 2014
Last update date Jan 09, 2018
Contact name Ann Harris
Organization name Northwestern University
Street address 2430 N Halsted
City Chicago
State/province Illinois
ZIP/Postal code 60614
Country USA
Platforms (1)
GPL17077 Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Probe Name version)
Samples (4)
GSM1477458 REP_ctr_rep1
GSM1477459 REP_ctr_rep2
GSM1477460 REP_R1881_rep1
This SubSeries is part of SuperSeries:
GSE59783 Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function
BioProject PRJNA258154

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Supplementary file Size Download File type/resource
GSE60381_RAW.tar 49.7 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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