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DRP002785
Mus musculus
4 Downloadable Samples
Illumina HiSeq 1500
Description
E13.5 Atm+/- pregnant mice were intraperitoneally injected with saline or etoposide 0.5 mg/kg consecutive three days, and scarified 24 hr after final injection. After genotyping, samples were subjected RNA sequencing. Total RNA was extracted from mice fetal liver. The libraries were then submitted for Illumina HiSeq1500 sequencing according to the standard operation. Paired-end 90 or 100 nucleotide reads were generated and checked for data quality using FASTQC. After etoposide treatment, various chimeric fusion mRNAs were observed in Atm wild type and deficient liver cells. The number of chimeric fusion mRNAs was much higher in Atm deficient fetal liver than wild type littermate. Mll-ptp4a2 fusion mRNA was identified from Atm deficient liver cells by etoposide exposure.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 214 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Comprehensive molecular and immunological characterization of hepatocellular carcinoma.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 198 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Hepatocellular carcinoma (HCC) is a heterogeneous disease with a variety of etiological factors, and ranks as the second leading cause of cancer-related mortality worldwide due to multifocal recurrence. Comprehensive molecular evaluation of HCC by multiplatform analysis defined three major subtypes: (1) mitogenic and stem cell-like tumors with chromosomal instability; (2) CTNNB1-mutated tumors displaying DNA hypermethylation; and (3) metabolic syndrome-associated tumors, which included an immunogenic subgroup characterized by macrophage infiltration and favorable prognosis. Although genomic and epigenomic analysis explicitly discriminated HCC with intrahepatic metastasis (IM) from multicentric HCC (MC), the phenotypic similarity between the primary and recurrent tumors was not linked to the IM/MC diagnosis, but rather the integrated classification. Thus, identification of these HCC subtypes provides insights into patient stratification and opportunities for therapeutic development.
Publication Title
Comprehensive molecular and immunological characterization of hepatocellular carcinoma.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 30 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
The entire small intestine was obseved by balloon endoscopy. Biopsy specimens were taken from jejunum, ileum and colon, respectively.
Publication Title
Reduced Human α-defensin 6 in Noninflamed Jejunal Tissue of Patients with Crohn's Disease.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 27 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Tongue squamous cell carcinoma (TSCC) varies in characteristics even in early stages and is mainly classified into three subtypes, which are superficial, exophytic and endophytic types, based on a macroscopic appearance of tumor growth.Of these subtypes, endophytic tumor has a poorer prognosis because of its invasive feature and higher frequency to have metastasis. To understand a molecular mechanism of endophytic subtype and identify biomarkers, we performed comprehensive microarray analysis for mRNAs from clinical biopsy sampleswhich were classified into subtypes and found overexpression of parvin-beta (PARVB) gene significantly related to endophytic type. PARVB is known to play a critical role in actin reorganization and focal adhesions. Knocking down PARVB expression in vitrocaused apparent decreases in cell migration and wound healing, implying that PARVB has a crucial role in cellular motility. Moreover, metastasis-free survival was significantly lowered in patients with higher PARVB expression. Therefore overexpression of PARVB is a candidate biomarker for endophytic tumor and metastasis and may be clinically applicable for decision making of an adjuvant therapy in TSCC.
Publication Title
PARVB overexpression increases cell migration capability and defines high risk for endophytic growth and metastasis in tongue squamous cell carcinoma.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Hepatocellular carcinoma (HCC) is a heterogeneous disease with a variety of etiological factors, and ranks as the second leading cause of cancer-related mortality worldwide due to multifocal recurrence. Comprehensive molecular evaluation of HCC by multiplatform analysis defined three major subtypes: (1) mitogenic and stem cell-like tumors with chromosomal instability; (2) CTNNB1-mutated tumors displaying DNA hypermethylation; and (3) metabolic syndrome-associated tumors, which included an immunogenic subgroup characterized by macrophage infiltration and favorable prognosis. Although genomic and epigenomic analysis explicitly discriminated HCC with intrahepatic metastasis (IM) from multicentric HCC (MC), the phenotypic similarity between the primary and recurrent tumors was not linked to the IM/MC diagnosis, but rather the integrated classification. Thus, identification of these HCC subtypes provides insights into patient stratification and opportunities for therapeutic development.
Publication Title
Comprehensive molecular and immunological characterization of hepatocellular carcinoma.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 11 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Macrophage-inducible C-type lectin (Mincle, Clec4e) is a pathogen sensor that recognizes pathogenic fungi and Mycobactrium tuberculosis. We perfomed microarray analysis using peritoneal macrophages stimulated with TDM, a mycobacterial cell wall glycolipid that is known to be a Mincle ligand.
Publication Title
Macrophage-inducible C-type lectin underlies obesity-induced adipose tissue fibrosis.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens, Rattus norvegicus
- 10 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Synovial and bone marrow mesenchymal stem cells after intradiscally injection show regenerative effects of nucleus pulposus.
Publication Title
Intradiscal transplantation of synovial mesenchymal stem cells prevents intervertebral disc degeneration through suppression of matrix metalloproteinase-related genes in nucleus pulposus cells in rabbits.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Under hypoxic condition, solid tumor cells are known to involve gene expressions for adopting low O2 condition. We examined chronic hypoxia environment of human rhabdomyosarcoma cell (SJRH30), which is important for understanding characteristic of cancer in the body.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The purpose of this study was to isolate NCSCs from oral mucosa using the neurosphere technique.
Publication Title
Sphere-Derived Multipotent Progenitor Cells Obtained From Human Oral Mucosa Are Enriched in Neural Crest Cells.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples