biostudies-arrayexpressL'Hôte DavidHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16651ERβ1 is the predominant isoform mediating transcriptional activity in granulosa cells; however, ERβ1-specific target genes remain largely unknown. Here, we performed transcriptomic analysis of primary human granulosa cells with specific knockdown of ERβ1 and stimulation with estradiol (E2), an ERβ agonist. ERβ1 knockdown was achieved by lentiviral transduction of shRNA specifically targeting the ERβ1 isoform, with scrambled shRNA used as a control. Cells were subsequently treated with 10 nM E2 or vehicle control for 24 h. Total RNA was extracted and sequenced on an Illumina NovaSeq 6000 platform using paired-end 150 bp reads.biostudies-arrayexpressLibrary Construction - Extracted RNA samples underwent quality control (QC) using the Agilent Bioanalyzer 2100 and were quantified with a Qubit Fluorometer (Thermo Fisher Scientific). cDNA library preparation and RNA sequencing were carried out by Novogene (Cambridge, UK). Libraries were prepared from 200 ng of input RNA and PCR-amplified indexedSequencing - libraries were sequenced on the Illumina NovaSeq 6000 platform (paired-end 150 bp reads), generating approximately 40 million reads per sample.Sample Collection - Five women undergoing in vitro fertilization treatment for infertility due to tubal or male factors at Antoine Béclère Hospital (Clamart, France) were included in this study. All patients underwent a standard gonadotropin-releasing hormone (GnRH) antagonist stimulation protocol. Follicular fluid containing granulosa cells was collected 36 h after administration of recombinant human chorionic gonadotropin via transvaginal ultrasound-guided aspiration. Informed written consent was obtained from all participants. Ethical approval was granted by the institutional review board (IRB Blefco-IORG0010582) under registration number “2021-1”. After oocyte retrieval, granulosa lutein cells (hGCs) were purified from the follicular fluid. Briefly, follicular fluid was centrifuged through a one-step Percoll gradient at 4,000 × g for 15 min to remove red blood cells. hGCs were collected at the interface, washed with DPBS, resuspended in growth medium, and cultured at 37°C in a humidified incubator with 5% CO₂. Viral infection and E2 treatment of primary cultures of granulosa cells: Primary cultured hGCs were seeded in 12-well plates at 0.6 × 106 cells per well in growing medium and maintained at 37°C for 24 h. Cells were then transduced with viral particles (ESR2-V1 (B1) targeting or scramble (S)) at a multiplicity of infection (MOI) of 90 viral particles per cell (optimized titer) in 250 µL of DMEM/F12 medium without phenol red. Three hours post-infection, treatment medium containing 2 µg/mL puromycin was added to ensure selection of successfully transduced cells. Twenty-four hours after transduction, cells were treated for an additional 24 hours with either vehicle (CT) or 10 nM E2 in fresh treatment medium containing puromycin.Nucleic Acid Extraction - Total RNA was extracted from each condition using the RNeasy® Micro KitOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw RNA-seq FASTQ files were processed for quality control and adaptor trimming using fastp (RRID: SCR_016962). Cleaned reads were aligned to the human reference genome (hg38) using HISAT2 version 2.0.5 within the Illumina BaseSpace RNA-seq Alignment application. These preprocessing and alignment steps were performed by Novogene (UK). Following alignment, gene-level read counts were generated from BAM files using a reference gene annotation (GENCODE, hg38), producing raw integer count matrices. These raw counts were used exclusively as input for downstream statistical analysis. Transcript abundance was additionally estimated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) using Cufflinks for descriptive purposes only and was not used for differential expression testing. Differential expression analysis comparing control (CT) and E2-treated patient samples (E2) was performed using DESeq2 (v1.40.2), which models raw count data using a negative binomial distribution and applies internal normalization for library size. Nominal p-values derived from DESeq2 were used for visualization in volcano plots, whereas adjusted p-values (Benjamini-Hochberg false discovery rate) were used to define significantly differentially expressed genes and to generate gene lists. Genes with log2(fold change) ≥ 1 and adjusted p-value ≤ 0.05 were considered significant.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensEstrogen receptor beta isoforms interplay integrates nuclear and extra-nuclear signaling to modulate human granulosa cell growthL'Hôte DavidChauvin StéphanieClémentine Marie, Inza-Noor Baskaran, Raphaël Corre , Anne Mayeur, Michaël Grynberg, , Guillaume Chevreux, David L’Hôte, Joëlle Cohen-Tannoudji and Stéphanie ChauvinfalseRNA-seq of human primary ovarian granulosa cells with knockdown of ESR2 isoform 1, treated with estradiolERβ1 is the predominant isoform mediating transcriptional activity in granulosa cells; however, ERβ1-specific target genes remain largely unknown. Here, we performed transcriptomic analysis of primary human granulosa cells with specific knockdown of ERβ1 and stimulation with estradiol (E2), an ERβ agonist. ERβ1 knockdown was achieved by lentiviral transduction of shRNA specifically targeting the ERβ1 isoform, with scrambled shRNA used as a control. Cells were subsequently treated with 10 nM E2 or vehicle control for 24 h. Total RNA was extracted and sequenced on an Illumina NovaSeq 6000 platform using paired-end 150 bp reads.2026-06-30T00:00:00Z2026-06-30T01:00:56.154Z2026-02-13T12:06:06.478ZE-MTAB-16651ERP189098EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184