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GSE63557
Mus musculus
30 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Balb/c mice were inoculated subcutaneously with AB1-HA cells on both flanks on day 0. The mice were then treated with anti-CTLA-4 on day 5 or 6.
Publication Title
Network analysis of immunotherapy-induced regressing tumours identifies novel synergistic drug combinations.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 14 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Cell based bone regeneration strategies offer promise for traumatic bone injuries, congenital defects, non-union fractures and other skeletal pathologies. Postnatal bone remodeling and fracture healing provide evidence that an osteochondroprogenitor cell is present in adult life which can differentiate to remodel or repair the fractured bone. However, cell based skeletal repair in the clinic is still in its infancy mostly due to poor characterization of progenitor cells and lack of knowledge about their in vivo behavior. Here we took a combined approach of high throughput screening, flow based cell sorting and in vivo transplantation to identify markers that identify osteochondroprogenitor cells. We show that the presence of tetraspanin CD9 enriches for osteochondroprogenitors within CD105+vemesenchymal cells and these cells readily form bone upon transplantation. In addition we have used Thy1.2 (CD90) and the ectonucleotidase CD73 to identify subsets within the CD9+ve population that lead to endochondral or intramembranous-like bone formation. Utilization of this unique cell surface phenotype to enrich for osteochondroprogenitor cells will allow for further characterization of the molecular mechanisms that regulate their osteogenic properties.
Publication Title
Tetraspanin CD9 and ectonucleotidase CD73 identify an osteochondroprogenitor population with elevated osteogenic properties.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 36 Downloadable Samples
Illumina HiSeq 2500
Description
We identified that downregulation of RNF20/H2Bub1 is involved in HGSOC progression through altering key immune signaling pathways. The goal of this RNA-seq is to analyze gene expression profile in FTSEC cells (FT190 and FT194 cell lines) with RNF20 knockdown (shRNF20) or control shRNA. Integrating the data from ATAC-seq for same samples, we observed that expression of immune signaling pathways have significantly changed by RNF20/H2Bub1 downregulation. Overall design: mRNA profiles of FT190 and FT194 shRNF20 (RNF20 knockdown) or control shRNA cells were generated by deep sequencing using Illumina HiSeq 2500, in triplicate.
Publication Title
Early Loss of Histone H2B Monoubiquitylation Alters Chromatin Accessibility and Activates Key Immune Pathways That Facilitate Progression of Ovarian Cancer.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Original patient tumor is directly implanted in mice xenografts. Tumor is propagated to multiple mice for conduct of 6 arm treatment trials and control. Therapies are selected based on T0 and F0 genomic profiles.
Publication Title
Using a rhabdomyosarcoma patient-derived xenograft to examine precision medicine approaches and model acquired resistance.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 2 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Adipose tissue iNKT cells have different functions than iNKT cells in the blood and other organs.
Publication Title
Regulatory iNKT cells lack expression of the transcription factor PLZF and control the homeostasis of T(reg) cells and macrophages in adipose tissue.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 50 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We used microarray-based expression genomics in 25 inbred mouse strains to identify dorsal root ganglion (DRG)-expressed genetic contributors to mechanical allodynia a prominent symptom of chronic pain.
Publication Title
The nicotinic α6 subunit gene determines variability in chronic pain sensitivity via cross-inhibition of P2X2/3 receptors.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 24 Downloadable Samples
- Illumina HiSeq 2000
Description
The transcriptional profile of A673 parental and SP-2509 Drug resistant cells treated with DMSO and SP-2509 (2uM 48hrs) Overall design: A673 parental and SP-2509 Drug resistant cells treated with DMSO and SP-2509 (2uM 48hrs)
Publication Title
Ewing sarcoma resistance to SP-2509 is not mediated through KDM1A/LSD1 mutation.
Sample Metadata Fields
Treatment, Subject
View Samples- Homo sapiens
- 9 Downloadable Samples
- Illumina HiSeq 2000
Description
The transcriptional profile of A673 parental, and SP-2509 drug resistant washout cells (4 and 6 months) Overall design: Following generation of A673 SP-2509 drug resistant cells (chronic exposure for 7 months), drug was withdrawn with cell pellets collected 4 and 6 months after removal.
Publication Title
Ewing sarcoma resistance to SP-2509 is not mediated through KDM1A/LSD1 mutation.
Sample Metadata Fields
Disease, Treatment, Subject
View Samples- Mus musculus
- 38 Downloadable Samples
- Illumina HiSeq 2500
Description
Numerous microRNAs and their target mRNAs are co-expressed across diverse cell types. However, it is unknown whether they are regulated in a cellular context-independent or -dependent manner. Here, we explored transcriptome-wide targeting and gene regulation by miR-155, whose activation-induced expression plays important roles in innate and adaptive immunity. Through mapping of miR-155 targets using differential Argonaute iCLIP, mRNA quantification with RNA-Seq, and 3'UTR usage analysis using polyadenylation (polyA)-Seq in activated miR-155-sufficient and deficient macrophages, dendritic cells, T and B lymphocytes, we identified numerous targets differentially bound by miR-155. While alternative cleavage and polyadenylation (ApA) contributed to differential miR-155 binding to some transcripts, in a majority of cases identical 3'UTR isoforms were differentially regulated across cell types, suggesting ApA-independent and cellular context-dependent miR-155-mediated gene regulation reminiscent of sequence-specific transcription factors. Our study provides comprehensive maps of miR-155 regulatory RNA networks and offers a valuable resource for dissecting context-dependent and -independent miRNA-mediated gene regulation in key cell types of the adaptive and innate immune systems. Overall design: Primary dendritic cells, B cells, CD4 T cells, and macrophages from C57BL/6J wild type and miR-155 KO mice were cultured in RPMI medium with 10% FBS. Prior to harvesting primary dendritic cells, mice were subcutaneously injected with one million B16 melanoma cells expressing Flt3 ligand for about two weeks. After purification of splenic CD11c+ dendritic cells by CD11c microbeads (Miltenyi Biotec), dendritic cells were activated in a medium containing 100 ng/ml LPS (SIGMA) and 20 ng/ml GMSCF (Tonbo). Splenic primary B cells were purified by negative selection using Dynabeads Mouse CD43 (Invitrogen), and activated in a medium containing 25 ug/ml LPS and 6.5 ng/ml mIL4 (PeproTech). CD4 T cells from lymph node and spleen were purified with Dynabeads FlowComp Kit (Invitrogen). CD4+CD25-CD44- T cells were then activated with Dynabeads Mouse T-Activator CD3/CD28 (Invitrogen). Intraperitoneal macrophages, induced by thioglycollate injection, were harvested and activated with 100 ng/ml LPS.
Publication Title
The effect of cellular context on miR-155-mediated gene regulation in four major immune cell types.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Mus musculus
- 24 Downloadable Samples
- Illumina HiSeq 2500
Description
Numerous microRNAs and their target mRNAs are co-expressed across diverse cell types. However, it is unknown whether they are regulated in a cellular context-independent or -dependent manner. Here, we explored transcriptome-wide targeting and gene regulation by miR-155, whose activation-induced expression plays important roles in innate and adaptive immunity. Through mapping of miR-155 targets using differential Argonaute iCLIP, mRNA quantification with RNA-Seq, and 3'UTR usage analysis using polyadenylation (polyA)-Seq in activated miR-155-sufficient and deficient macrophages, dendritic cells, T and B lymphocytes, we identified numerous targets differentially bound by miR-155. While alternative cleavage and polyadenylation (ApA) contributed to differential miR-155 binding to some transcripts, in a majority of cases identical 3'UTR isoforms were differentially regulated across cell types, suggesting ApA-independent and cellular context-dependent miR-155-mediated gene regulation reminiscent of sequence-specific transcription factors. Our study provides comprehensive maps of miR-155 regulatory RNA networks and offers a valuable resource for dissecting context-dependent and -independent miRNA-mediated gene regulation in key cell types of the adaptive and innate immune systems. Overall design: Primary dendritic cells, B cells, CD4 T cells, and macrophages from C57BL/6J wild type and miR-155 KO mice were cultured in RPMI medium with 10% FBS. Prior to harvesting primary dendritic cells, mice were subcutaneously injected with one million B16 melanoma cells expressing Flt3 ligand for about two weeks. After purification of splenic CD11c+ dendritic cells by CD11c microbeads (Miltenyi Biotec), dendritic cells were activated in a medium containing 100 ng/ml LPS (SIGMA) and 20 ng/ml GMSCF (Tonbo). Splenic primary B cells were purified by negative selection using Dynabeads Mouse CD43 (Invitrogen), and activated in a medium containing 25 ug/ml LPS and 6.5 ng/ml mIL4 (PeproTech). CD4 T cells from lymph node and spleen were purified with Dynabeads FlowComp Kit (Invitrogen). CD4+CD25-CD44- T cells were then activated with Dynabeads Mouse T-Activator CD3/CD28 (Invitrogen). Intraperitoneal macrophages, induced by thioglycollate injection, were harvested and activated with 100 ng/ml LPS. Each condition has 3 sequencing replicates.
Publication Title
The effect of cellular context on miR-155-mediated gene regulation in four major immune cell types.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples