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GSE25652
Bos taurus, Ovis aries
10 Downloadable Samples
Affymetrix Bovine Genome Array (bovine)
Description
Background Correct achievement of early ovarian folliculogenesis is a crucial phase for further ovarian function. This process is closely regulated by cell-cell interactions and coordinated expression of genes from oocyte and granulosa cells. But, despite of the large number of studies, little is known about the precise gene expression patterns driving early folliculogenesis. The experimental limitations concerned the very small size of these follicles and the mixture of the different developmental stages within an ovary that make the study of isolated follicular components much more difficult. The recently developed laser capture microdissection (LCM) technique coupled with microarrays experiments is promising in addressing the molecular specificity of each follicular compartment. Nevertheless, the isolation of unique cells or group of cells is still challenging to maintain RNA quality during this process and to obtain sufficient amount of RNA. In this study, we described a method allowing the analysis of oocyte and granulosa cells gene expression during the first stages of sheep early folliculogenesis. Results First we developed a new fixation protocol using a frizzed 70% ethanol fixation solution that ensures correct single cell capture and RNA integrity during microdissection time. After LCM capture of the compartments and follicular stages, RNA extraction and amplification, the expression of 6 oocyte-specific genes (SOHLH2, MAEL, MATER, VASA, GDF9, BMP15) and 3 granulosa cell-specific genes (KITLG, GATA4, AMH) confirmed the purity of the samples and documented their ovine expression profiles. Then, using bovine Affymetrix chip, we identified for the first time, a global gene expression for each follicular compartment during early developmental stages. Particularly the granulosa cell data set is quite unique. 1050 granulosa cell specific transcripts compared to oocyte and 759 oocyte specific transcripts were detected. The analysis of the expression of 2 genes (SIRT7, FST) confirmed this specificity of expression. Finally, the integration of the data stated the 3 main physiological events involved in early folliculogenesis and provided descriptive elements that confirmed the relevance and the potential of the LCM-derived RNAs. Conclusions This method should contribute through an additional genome wide expression profiling to give insights on molecular mechanisms involved in stage transitions and cell type interplays.
Publication Title
Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by laser capture microdissection.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We compare transcriptomic profiles of human induced pluripotent stem cells (iPSCs), motor neurons (MNs) in vitro differentiated from iPSCs or human ESCs containing a HB9::GFP reporter for MNs, and human fetal spinal cords.
Publication Title
ALS disrupts spinal motor neuron maturation and aging pathways within gene co-expression networks.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Background: Gliomas are the most common type of primary brain tumours, and in this group glioblastomas (GBMs) are the higher-grade gliomas with fast progression and unfortunate prognosis. Two major aspects of glioma biology that contributes to its awful prognosis are the formation of new blood vessels through the process of angiogenesis and the invasion of glioma cells. Despite of advances, two-year survival for GBM patients with optimal therapy is less than 30%. Even in those patients with low-grade gliomas, that imply a moderately good prognosis, treatment is almost never curative. Recent studies have demonstrated the existence of a small fraction of glioma cells with characteristics of neural stem cells which are able to grow in vitro forming neurospheres and that can be isolated in vivo using surface markers such as CD133. The aim of this study was to define the molecular signature of GBM cells expressing CD133 in comparison with non expressing CD133 cells. This molecular classification could lead to the finding of new potential therapeutic targets for the rationale treatment of high grade GBM.
Publication Title
Molecular analysis of ex-vivo CD133+ GBM cells revealed a common invasive and angiogenic profile but different proliferative signatures among high grade gliomas.
Sample Metadata Fields
Specimen part, Disease
View Samples- Mus musculus
- 38 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Numerous CD11b+ myeloid cells are present within the dermis. They are very heterogeneous and can be divided in dermal DCs, tissue monocytes and tissue macrophages. At steady state, only CD11b+ DC migrate from the dermis to the skin draining lymph nodes whereas upon DNFB-induced inflammation, CD11b+ DC as well as dermal monocytes migrated to the lymph nodes. The objective of this study was to use gene expression profiling to rigorously identify the different subsets of dermal CD11b+ myeloid cells at steady state and upon inflammation and to characterize their functional potential.
Publication Title
Origins and functional specialization of macrophages and of conventional and monocyte-derived dendritic cells in mouse skin.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
Illumina HiSeq 2500
Description
We report the RNAseq data obtained from 50.000-100.000 CD31-/CD45- pneumocytes isolated by FACS from mice harboring a normal dose or one extra copy of the Sirt1 gene, and a tamoxifen-inducible oncogenic KI alelle of KRasG12V after 4 weeks of tamoxifen treatment. Pneumocytes with the activated form of the inducible KRasG12V oncogene sere selected making use of the reporter gene LacZ (located next to the oncogene in the same polycistronic mRNA), by loading CD31-/CD45- pneumocytes with the LacZ-activated fuorogenic molecule FDG prior to FACS sorting. Overall design: Four replicates of each genetic group (Sirt1-WT and Sirt1-Tg) pneumocytes were used for this study. Sirt1-WT were used as reference controls.
Publication Title
Sirt1 protects from K-Ras-driven lung carcinogenesis.
Sample Metadata Fields
Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
We report the RNAseq data obtained from 50.000-100.000 CD31-/CD45- pneumocytes isolated by FACS from mice harboring a normal dose or one extra copy of the Sirt1 gene, and a tamoxifen-inducible oncogenic KI alelle of KRasG12V after 4 weeks of tamoxifen treatment plus 2 weeks without tamoxifen. Pneumocytes with the activated form of the inducible KRasG12V oncogene sere selected making use of the fluorescent reporter gene Katushka (located at an independent locus), by detecting Katushka fluorescence. Overall design: Four replicates of each genetic group (Sirt1-WT and Sirt1-Tg) pneumocytes were used for this study. Sirt1-WT were used as reference controls.
Publication Title
Sirt1 protects from K-Ras-driven lung carcinogenesis.
Sample Metadata Fields
Sex, Subject
View Samples- Homo sapiens
- 14 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Phenotypic, transcriptomic, and genomic features of clonal plasma cells in light-chain amyloidosis.
Sample Metadata Fields
Specimen part, Disease
View Samples- Homo sapiens
- 14 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Immunoglobulin light-chain amyloidosis (AL) is a rare clonal plasma cell (PC) disorder that remains largely incurable. AL and multiple myeloma (MM) share the same cellular origin, but while knowledge about MM PC biology has improved significantly, the same does not apply for AL. Here, we undertook an integrative phenotypic, molecular, and genomic approach to study clonal PCs from 22 newly-diagnosed AL patients. Through principal-component-analysis, we demonstrated highly overlapping phenotypic profiles between AL and MGUS or MM patients. However, in contrast to MM, highly-purified FACSs-sorted clonal PCs in AL (n=9/22) show virtually normal transcriptomes with only 68 deregulated genes as compared to normal PCs, including a few tumor suppressor (CDH1, RCAN) and pro-apoptotic (GLIPR1, FAS) genes. Notwithstanding, clonal PCs in AL (n=11/22) were genomically unstable with a median of 9 copy-number-abnormities (CNAs) per case; many of which similar to those found in MM. Whole-exome sequencing (WES) was performed in three AL patients and revealed a median of 10 non-recurrent mutations per case. Altogether, we showed that although clonal PCs in AL display phenotypic and CNA profiles similar to MM, their transcriptome is remarkably similar to that of normal PCs. First-ever WES revealed the lack of a unifying mutation in AL
Publication Title
Phenotypic, transcriptomic, and genomic features of clonal plasma cells in light-chain amyloidosis.
Sample Metadata Fields
Specimen part, Disease
View Samples- Homo sapiens
- 15 Downloadable Samples
- IlluminaHiSeq2000
Description
Identification of the counterpart protein of Nef during HIV infection
Publication Title
HIV-1 Nef promotes infection by excluding SERINC5 from virion incorporation.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
The objective of the study was to evalute the changes in gene expression associated to UCP2 invalidation in colon tumors from AOM/DSS-treated mice
Publication Title
UCP2 Deficiency Increases Colon Tumorigenesis by Promoting Lipid Synthesis and Depleting NADPH for Antioxidant Defenses.
Sample Metadata Fields
Specimen part
View Samples