Ontology highlight
ABSTRACT:
PROVIDER: PRJNA925873 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23157137_1.fastq.gz | Fastqsanger.gz | |||
| SRR23157137_2.fastq.gz | Fastqsanger.gz | |||
| SRR23157138_1.fastq.gz | Fastqsanger.gz | |||
| SRR23157138_2.fastq.gz | Fastqsanger.gz | |||
| SRR23157139_1.fastq.gz | Fastqsanger.gz |
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Project description:The goal of this experiment was to determine differences in RNA expression between the central necrotic tumor core and the non-necrotic rim region in orthotopic xenograft models of 4T1 cells transplanted into immunocompromised rat hosts. These samples are derived from tissues obtained from 4T1 spheroids transplanted orthotopically into the mammary fat pads of SRG OncoRats. 4T1 cells were cultured as spheroids in suspension for 24-hours prior to transplantation in 2% matrigel. 600,000 cells in a 1:1 mixture of matrigel and DMEM/F12 were transplanted orthotopically into the right T4 fat pads of SRG rats. At day 27 post transplanation, primary tumors and lungs were collected. The primary tumors were cut in half to expose the cross-section, and the tumors were dissected to isolate the necrotic core region and the non-necrotic rim region. Samples were snap frozen and sent to Genewiz-Azenta for RNA extraction, library prep, and next-gen sequencing.
2024-01-01 | GSE223419 | GEO
Project description:These samples are derived from tissues obtained from 4T1 spheroids transplanted orthotopically into the mammary fat pads of SRG OncoRats. 4T1 cell lines were established by viral transduction that stably express either a non-targeting control shRNA (NT4) or an shRNA targeting Angptl-7. 4T1 cells were cultured as spheroids in suspension for 24-hours prior to transplantation in 2% matrigel. 600,000 cells in a 1:1 mixture of matrigel and DMEM/F12 were transplanted orthotopically into the right T4 fat pads of SRG rats. At day 27 post transplanation, primary tumors. The primary tumors were cut in half to expose the cross-section, and the tumors were dissected to isolate the necrotic core region and the non-necrotic rim region. Samples were snap frozen and sent to Genewiz-Azenta for RNA extraction, library prep, and next-gen sequencing.
2024-01-01 | GSE224232 | GEO
Project description:Single cell RNA-seq of 4T1 mammary tumors
| PRJNA962048 | ENA
Project description:Glioblastoma multiforme (GBM), the most advanced form of a large subset of brain tumors collectively known as glioma, is the most aggressive and invasive type of brain tumor. Patients usually experience a median survival range of 9 to 12 months. GBMs are extremely difficult to manage because of the tumor cellsâ tendency to migrate and pervade into adjacent tissues. Surgical resection of GBMs generally only slows disease progression because any remaining tumor cells proceed to migrate through brain tissues and reform a new tumor mass. It is hypothesized that the invasive phenotype of these tumor cells may be attributable to unique gene expression. Stationary core and invasive rim tumor cells were collected separately by laser capture microdissection (LCM) from 19 biopsy samples. Identification of differentially expressed genes in the tumor core and invasive rim can give valuable insight to the genes and pathways potentially involved with the invasive phenotype. This information can then be used to generate possible biomarkers, diagnostic markers, or drug targets. Human glioblastoma tumor samples were obtained from patients who underwent primary therapeutic brain tumor resection. All specimens were collected and submitted to the study under institutional review board approved protocols. None of the patients had been subjected to chemotherapy or radiotherapy prior to resection, in order to avoid genetic signatures that are due to exposure to alkylating agents and/or ionizing radiation. All specimens were verified as GBMs by a neuropathologist. Tumors are embedded in OCT, then sectioned in a cryostat at -20C, to a thickness of 8-10 um and placed onto HistoGene slides. Sections to be microdissected are removed from the -80C fixed and stained with an abbreviated Hematoxylin and Eosin protocol. Two thousand tumor core and invasive cells are dissected onto separate caps using the PixCell II instrument using CapSure⢠Macro LCM Caps. The CapSure⢠Macro LCM Caps LCM 0211 should be used with the AutoPix instrument. Cells in the tumor core are identified by nuclear atypia and size and captured using the larger spot sizes. Tumor cells immediately adjacent to necrotic areas, cortical areas, cells with small regular nuclei, endothelial and blood cells should be avoided. Individual white matter invading GBM cells can be identified by means of their nuclear atypia and heteropyknotic staining, which is consistent with that of the cells within the tumor core. They should be microdissected using the 7.5 um laser spot size and the initial power settings recommended by the PixCell II manual. After microdissection all harvested material should immediately be lysed on the cap by applying the lysis buffer (XB) from the PicoPure RNA Isolation Kit according to the PicoPure protocol and stored -80C. Cell populations harvested on different caps can be pooled at the time of RNA isolation. RNA integrity is varified by identification of distinct 28S and 18S ribosomal bands with an Agilent Bioanalyzer using the RNA 6000 Nano LabChip kit. Total RNA was isolated from 2000 LCM cells (to ensure at least 500 ng total RNA) using the PicoPure RNA solation Kit, following manufacturers protocol. mRNA is reverse transcribed with the RiboAmp RNA Amplification kit. 500 ng total RNA is amplified with the RiboAmp RNA Amplification kit, following manufacturerâs instructions. The total yield that can be expected falls between 30 and 60 µg copy RNA. The size of the copy RNA should be verified by gel electrophoresis. Approximately 500ng of copy RNA can be separated on a 1% agarose gel in TAE buffer. A smear of amplified material should be seen between 200 and 3000bp. Six µg amplified RNA are labeled in a RT with SuperScriptIII in the presence of dUTP Cy5 utilizing 6 µg random hexamers as primers. Universal reference RNA is amplified one round in the same manner and labeled with Cy3 dUTP. Labeled cDNA is hybridized overnight onto cDNA microarray. Following hybridization, arrays are washed, scanned and quantitated with the Axon GenePix 4000 microarray reader (Axon Instruments). Gene expression results are analyzed using GeneSpring (Silicon Genetics) software. Intensity dependent normalization is applied, where the ratio is reduced to the residual Lowess fit of the intensity versus ratio curve. The measured intensity of each gene is divided by its reference channel (signal from the universal reference RNA) in each sample. When the reference channel is below 10, the data point is considered uninformative. The ratios (sample over reference) for the tumor core experiments and invasive rim experiments are averaged and compared. Genes that are more than two-fold differentially regulated in the majority of the matched core/invasive rim sets are selected.
2010-05-18 | E-GEOD-12689 | biostudies-arrayexpress
Project description:We have previously described a sub-clones of the 4T1 mammary carcinoma cell line that are proficient for vasculogenic mimciry (VM), namely 4T1-E and 4T1-T. In vitro assays suggest that not all cells within these lines a VM-competent. To explore subsets of cells within tumors derived from these cells that may display VM properties we utilized single cell RNA-Seq of 4T1-T mammary fat-pad tumors.
2023-07-26 | GSE230642 | GEO
Project description:The present study was designed to identify genes induced by irradiation in the 4T1 breast cancer model mimicking aggressive local relapse after radiotherapy. For this purpose, we obtained the transcriptomes of 4T1 tumors grown in either preirradiated (IRR+4T1) or non-irradiated (4T1) mammary tissue.
2017-08-31 | GSE64193 | GEO
Project description:Tumors were harvested at day 24 post tumor cell engraftment and dissociated into single-cell suspensions. RFP-positive 4T1 cells were isolated by fluorescence-activated cell sorting (FACS). RNA was extracted using the RNeasy Mini Kit. Three independent RNA preparations from cultured 4T1-Luc2-RFP cells and FACS-isolated 4T1-Luc2-RFP cells were submitted for RNA sequencing analysis.
2019-04-02 | GSE129106 | GEO
Project description:The study aimed to analyse the transcriptome of mouse cancer cells while in primary tumor, in circulation and after homing to metastatic site. The model used here is the 4T1 cancer cell orthotopic model. GFP-labeled 4T1 breast cancer cells were orthotopically implanted in the mammary pads of mice. In this mouse model for breast cancer, primary breast tumors emerge following injection of cancer cells in the breast pad of female mice and subsequently develop lung metastases with 100% penetrance. Circulating cancer cells (CCC) and cancer cells from the primary tumors (PCC) and metastatic lungs (MCC) were FACS purified and their transcriptome assayed by gene expression microarray. RNA was extracted from PCC, MCC, and CCC using RNeasy Plus Mini Kit (Qiagen) and submitted to the Molecular Genetics Core Facility at Children’s Hospital (Boston, MA). Microarray analysis was performed using Mouse Ref8 Gene Expression BeadChip (Illumina platform).
2014-09-23 | E-GEOD-37344 | biostudies-arrayexpress
Project description:Analysis of rat tumor xenografts revealed genes that are upregulated in tumors expressing EGFRvIII
2015-09-08 | GSE51147 | GEO
Project description:Novel therapies targeting cancer stem cells (CSCs), which play critical roles in chemo- and radio-resistance, metastasis, and possibly resistance against cancer immunotherapy including granulocyte-macrophage colony-stimulating factor (GM-CSF) gene-transduced tumor cell vaccines, may provide beneficial clinical outcomes. Here, we used syngeneic immunocompetent mice that allowed precise evaluation of the immunogenicity of the side population (SP) isolated from 4T1 murine breast carcinoma (4T1-SP) cells as putative CSCs. 4T1-SP cells showed various stem cell properties including high capacities for colony formation and tumorigenicity as well as high expression of phosphorylated signal transducer and activator of transcription-3 and vascular endothelial growth factor that are inductive of immune tolerance. Despite these progressive malignant characteristics of 4T1-SP cells, subcutaneous injection of non-transmissible Sendai virus-mediated GM-CSF gene-transduced 4T1-SP (4T1-SP/GM) cells remarkably impaired their tumorigenicity compared with that of the controls. This impairment of tumorigenicity was partially dependent on CD8+ T cells in concert with CD4+ T cells and natural killer cells. Notably, therapeutic vaccinations using irradiated 4T1-SP/GM cells markedly suppressed tumor development of subcutaneously transplanted 4T1-SP cells compared with that of the controls including irradiated 4T1-non-SP/GM cells. Tumor suppression was accompanied by robust accumulation of mature dendritic cells at vaccination sites and systemic Th1-based cellular immunity. Moreover, vaccinations comprising primary 4T1-SP cells isolated from transplanted 4T1-SP tumors elicited antitumor effects. cDNA microarray analysis showed that 4T1-SP cells predominantly expressed genes of cancer-related antigens including cancer/testis antigens. Collectively, we demonstrate that SP cell-based vaccinations induce effective antitumor immunity that may improve the efficacy of SP cell-based immunotherapy. Gene expression profiles were compared between sorted 4T1-SP and 4T1-NSP cells.
2014-04-01 | E-GEOD-53444 | biostudies-arrayexpress