Ontology highlight
ABSTRACT:
PROVIDER: PRJNA555182 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9701540_1.fastq.gz | Fastqsanger.gz | |||
| SRR9701540_2.fastq.gz | Fastqsanger.gz | |||
| SRR9701550_1.fastq.gz | Fastqsanger.gz | |||
| SRR9701550_2.fastq.gz | Fastqsanger.gz | |||
| SRR9701531_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:RNA sequencing dataset for primary and recurrent ovarian granulosa cell tumors consists of 24 .bam files with aligned reads, including 8 primary and 16 recurrent tumors.
Total RNA was extracted from cryopreserved tissue of adult-type granulosa cell tumor samples. Libraries were prepared from cDNA using the NuGEN Ovation Ultralow Library System V2 (San Carlos, CA). Paired-end bulk RNA sequencing was performed on the Illumina HiSeq 2000 platform. RNA sequencing reads were aligned to the hg19/GRCh37 reference human genome using the STAR software (version 2.6.0b) with default parameters.
Samples description:
GCT001 Adult-type Granulosa Cell Tumor: recurrent tumor
GCT002 Adult-type Granulosa Cell Tumor: primary tumor
GCT003 Adult-type Granulosa Cell Tumor: recurrent tumor
GCT004 Adult-type Granulosa Cell Tumor: primary tumor
GCT005 Adult-type Granulosa Cell Tumor: recurrent tumor
GCT006 Adult-type Granulosa Cell Tumor: recurrent tumor
GCT007 Adult-type Granulosa Cell Tumor: primary tumor
GCT008 Adult-type Granulosa Cell Tumor: recurrent tumor
GCT009 Adult-type Granulosa Cell Tumor: recurrent tumor
GCT010 Adult-type Granulosa Cell Tumor: recurrent tumor
GCT011 Adult-type Granulosa Cell Tumor: primary tumor
GCT012 Adult-type Granulosa Cell Tumor: recurrent tumor
GCT013 Adult-type Granulosa Cell Tumor: recurrent tumor
GCT014 Adult-type Granulosa Cell Tumor: recurrent tumor
GCT015 Adult-type Granulosa Cell Tumor: recurrent tumor
GCT016 Adult-type Granulosa Cell Tumor: recurrent tumor
GCT017 Adult-type Granulosa Cell Tumor: recurrent tumor
GCT018 Adult-type Granulosa Cell Tumor: primary tumor
GCT019 Adult-type Granulosa Cell Tumor: recurrent tumor
GCT020 Adult-type Granulosa Cell Tumor: primary tumor
GCT021 Adult-type Granulosa Cell Tumor: primary tumor
GCT022 Adult-type Granulosa Cell Tumor: recurrent tumor
GCT023 Adult-type Granulosa Cell Tumor: recurrent tumor
GCT024 Adult-type Granulosa Cell Tumor: primary tumor
| EGAD00001009108 | EGA
Project description:FOXL2 is a transcription factor that plays a key role in sex determination, ovary development and maintenance. Mutations related to this gene have been described in syndromes involving premature ovarian failure and granulosa cell tumors. This kind of rare cancer (less than 5% of diagnosed ovarian cancers) has been causally associated with the FOXL2 c.402C>G, p.C134W mutation in 97% of the adult cases (AGCTs). In this study, we have used CRISPR technology to specifically eliminate the FOXL2 c.402C>G mutation in granulosa tumor cells. Our results indicate that this Cas9-mediated strategy allows the specific elimination of the mutation with no activity on the wild type allele. Granulosa cells depleted on FOXL2 c.402C>G show a reduced malignant phenotype. Specifically, we detect changes in cell proliferation, invasion, and cell death levels. In addition, we show that granulosa tumor cells become more susceptible to Dasatinib and Ketoconazole treatments when FOXL2 c.402C>G allele is eliminated. Our transcriptomic and proteomic analyses indicate that CRISPR-modified granulosa tumor cells significantly change their expression signature towards a wild type like phenotype. Finally, this expression signature has led us to discover new compounds with antiproliferative and proapoptotic effects on granulosa cell tumor cells. Our results demonstrate the potential of CRISPR for specifically targeting and eliminating a granulosa cell tumor-causing mutation, as well as its therapeutic potential for the treatment of this rare ovarian cancer.
2025-03-15 | PXD053682 | Pride
Project description:RNA was extracted from normal human granulosa cells from IVF patients (hGC1 and hGC2 samples) and from adult-type ovarian granulosa cell tumor samples (H1, H8, H20, H23, H24, H28, H30, H33, H4, H18) as described in Jamieson et al, 2010. RNA from all samples was linearly amplified using the Whole Transcriptome Amplification kit (Sigma), starting from 300ng of RNA, and with 12 amplifications cycles. cDNA was purified on columns and sent to the Nimblegen platform for hybridization and transcriptional profiling. The FOXL2 locus was gentoyped in tumor samples, and all samples were found positive for the recurrent somatic mutation p.Cys134Trp which is present in >95% of adult-type ovarian granulosa cell tumors (Shah et al, 2009).
2012-08-02 | E-MTAB-483 | biostudies-arrayexpress
Project description:Granulosa cell tumors (GCTs) are a rare form of stromal cell malignant cancer accounting for one in twenty cases of ovarian cancer. More than 400 tumors from aGCT patients of diverse ethnicities showed one single mutation in the Forkhead box L2 transcription factor gene FOXL2: Cys134Trp (c.402C<G). In this work, seeking more comprehensive profiling of the mutant FOXL2C134W transcriptomic activity in a model of adult Granulosa Cell Tumor (aGTC), we performed an RNA-seq analysis comparing the effect of FOXL2WT/SMAD3 and FOXL2C134W/SMAD3 overexpression in presence/absence of FOXO1 in an established human GC line (HGrC1).
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Project description:Single cell RNA-seq (scRNA-seq) from Trim28 ovary knockout and wildtype mice ovaries and testis to help elucidate the function of Trim28 in the adult mouse ovaries. The analysis revealed that loss of Trim28 in the adult mouse ovaries lead to a transcriptional repogramming of the Granulosa cells towards the Sertoli cell fate. Therefore, Trim28 has a function to maintain the adult ovarian cell identity
2022-05-24 | GSE166444 | GEO
Project description:FOXL2 is a transcription factor essential for sex determination and ovary development and maintenance. Mutations in this gene are implicated in syndromes involving premature ovarian failure and granulosa cell tumors (GCTs). This rare cancer accounts for less than 5% of diagnosed ovarian cancers and is causally associated with the FOXL2 c.402C>G, p.C134W mutation in 97% of the adult cases (AGCTs). In this study, we employed CRISPR technology to specifically eliminate the FOXL2 c.402C>G mutation in granulosa tumor cells. Our results show that this Cas9-mediated strategy selectively targets the mutation without affecting the wild-type allele. Granulosa cells lacking the FOXL2 c.402C>G exhibit a reduced malignant phenotype, with significant changes in cell proliferation, invasion, and cell death. Furthermore, these modified cells are more susceptible to Dasatinib and Ketoconazole. Transcriptomic and proteomic analyses reveal that CRISPR-modified granulosa tumor cells shift their expression profiles towards a wild-type like phenotype. Additionally, this altered expression signature has led to the identification of new compounds with antiproliferative and pro-apoptotic effects on granulosa tumor cells. Our findings demonstrate the potential of CRISPR technology for the specific targeting and elimination of a mutation causing granulosa cell tumors, highlighting its therapeutic promise for treating this rare ovarian cancer.
2025-04-16 | GSE271552 | GEO
Project description:Granulosa cell proliferation and differentiation are essential for follicle development. Breast cancer amplified sequence 2 (BCAS2) is necessary for spermatogenesis, oocyte development, and maintaining the genome integrity of early embryos in mice. However, the function of BCAS2 in granulosa cells is still unknown. We show that conditional disruption of BCAS2 causes follicles development failure; cell proliferation markers PCNA and Ki67 positive cell ratio are unchanged in granulosa cells. However, specific deletion of BCAS2 causes BrdU positive cell ratio to decrease, cell cycle arrest appearance, DNA damage, and cell apoptosis increase in granulosa cells, RPA1 was abnormally stained in granulosa cells. Furthermore, RNA-Seq results reveal that knockout of BCAS2 results in cellular senescence gene unusual expression. BCAS2 participates in the PRP19 complex to mediate alternative splicing (AS) of E2f3 and Flt3l mRNA to inhibit the cell cycle. Knock down of BCAS2 results in a significantly decrease of BrdU positive cell ratio in Human granulosa-like tumor(KGN) cell line. Thus, BCAS2 regulates granulosa cell proliferation, DNA damage repair, and cell apoptosis. BCAS2 is vital for female fertility.
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Project description:mRNA expression profiling in human granulosa cell tumor cell line and normal granulosa cells
2012-01-26 | E-MTAB-957 | biostudies-arrayexpress
Project description:RNA-SEQ data from 3 recurrent and 1 ovarian primary Granulosa Cell Tumour samples
| EGAD00000000046 | EGA
Project description:The Forkhead Box, FOXO1 and FOXO3, transcription factors regulate multiple functions in mammalian cells. Selective inactivation of the Foxo1 and Foxo3 genes in murine ovarian granulosa cells severely impairs follicular development and apoptosis causing infertility, and as shown herein, granulosa cell tumor (GCT) formation. Coordinate depletion of the tumor suppressor Pten gene in the Foxo1/3 strain enhanced the penetrance and onset of GCT formation A direct comparison of ovarian granulosa cells from wild type d25 and FOXO/PTEN knockout granulosa cell tumors.
2015-06-17 | E-GEOD-67662 | biostudies-arrayexpress