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Series GSE102396 Query DataSets for GSE102396
Status Public on Feb 15, 2018
Title Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone [ATAC-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The LβT2 mouse pituitary cell line has many characteristics of a mature gonadotrope and is a widely used model system for studying developmental processes and the response to gonadotropin-releasing hormone (GnRH). The global epigenetic landscape, which contributes to cell-specific gene regulatory mechanisms, and the single-cell transcriptome response variation of LβT2 cells have not been previously investigated. Here, we integrate the transcriptome and genome-wide chromatin accessibility state of LβT2 cells during GnRH stimulation. Additionally, we examine cell-to-cell variability in the transcriptional response to GnRH using gel-in-emulsion Drop-seq technology. Analysis of a bulk RNA-seq dataset obtained 45 minutes after exposure to either GnRH or vehicle identified 112 transcripts that were regulated > 4-fold by GnRH (FDR < 0.05). The top regulated transcripts constitute, as determined by Bayesian massive public data integration analysis, a human pituitary-relevant coordinated gene program. Chromatin accessibility (ATAC-seq) datasets generated from GnRH-treated LβT2 cells identified more than 58,000 open chromatin regions, some containing notches consistent with bound transcription factor footprints. Study of the most prominent open regions showed that 75% were in transcriptionally active promoters or introns, supporting their involvement in active transcription. Lhb, Cga, and Egr1 showed significantly open chromatin over their promoters. While Fshb was closed over its promoter, several discrete significantly open regions were found at -40 to -90 kb, which may represent novel upstream enhancers. Chromatin accessibility determined by ATAC-seq was associated with high levels of gene expression determined by RNA-seq. We obtained high quality single-cell gel-in-emulsion Drop-seq transcriptome data, with an average of >4000 expressed genes/cell, from 1992 vehicle- and 1889 GnRH-treated cells. While the individual cell expression patterns showed high cell-to-cell variation, representing both biological and measurement variation, the average expression patterns correlated well with bulk RNA-seq data. Computational assignment of each cell to its precise cell cycle phase showed that the response to GnRH was unaffected by cell cycle. To our knowledge, this study represents the first genome-wide epigenetic and single-cell transcriptomic characterization of this important gonadotrope model. The data have been deposited publicly and should provide a resource for hypothesis generation and further study.
Overall design ATAC-seq was performed on two replicate samples of LβT2 cells treated with 2 nM GnRH pulses every 2 h for a duration of 6 h and 45 min (4 pulses in total; cells harvested 45 min after last pulse) in a high throughput GnRH pulse system.
Contributor(s) Ruf-Zamojski F, Fribourg M, Ge Y, Nair V, Pincas H, Zaslavsky E, Nudelman G, Tuminello SJ, Watanabe H, Turgeon JL, Sealfon SC
Citation(s) 29487567
Submission date Aug 09, 2017
Last update date Jul 25, 2021
Contact name Frederique Ruf-Zamojski
Organization name Mount Sinai Medical Center
Department Neurology
Lab Sealfon
Street address 1468 Madison Avenue
City New York
State/province NY
ZIP/Postal code 10029
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (2)
GSM2736002 Rep1 + GnRH
GSM2736003 Rep2 + GnRH
This SubSeries is part of SuperSeries:
GSE102480 Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone
BioProject PRJNA397652
SRA SRP115078

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Supplementary file Size Download File type/resource
GSE102396_RAW.tar 1.8 Mb (http)(custom) TAR (of NARROWPEAK)
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Raw data are available in SRA
Processed data provided as supplementary file

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