publication_authors:Aihara H Results

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Rna-seq (51)

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Illumina HiSeq 2500 (29)

Illumina HiSeq 1500 (12)

Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2) (10)

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Includes Publication (51)

SRP064782

Arabidopsis thaliana circadian clock

Arabidopsis thaliana
12 Downloadable Samples
Illumina HiSeq 1500

Description

Study of the Arabidopsis circadian clock.

Publication Title

A hierarchical multi-oscillator network orchestrates the Arabidopsis circadian system.

Sample Metadata Fields

Specimen part

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SRP080962

Hepatic differentiation of liver organoids

Homo sapiens
29 Downloadable Samples
Illumina HiSeq 2500

Description

We analyzed gene expression profiles of self-organizing, multi-cellular, 3D liver organoids derived by co-culture of induced Pluripotent Stem Cell and stromal progenitors. We report the RNA-seq results of liver organoid at day0, day2, day4, day6 of co-culture. We also report RNA-seq results of constituent of the liver organoid, which are human iPSC at hepatic specification stage, human Mesenchymal stem cells derived from bone marrow, human umbilical vein endothelial cell. As controls, we also report RNS-seq results of un-differentiated human iPSC, human iPSC at definitive endoderm stage, human liver tissue, and primary cultured human hepatocytes isolated from unused donor livers. Overall design: mRNA profiles of liver organoids and their constituents were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

Publication Title

Paracrine signals regulate human liver organoid maturation from induced pluripotent stem cells.

Sample Metadata Fields

Subject, Time

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GSE93050

Tumor suppressor functions of DAXX through histone H3.3 deposition pathway in pancreatic neuroendocrine tumor

Homo sapiens
4 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Purpose: Pancreatic neuroendocrine tumors (PanNETs) have considerable malignant potential. Frequent somatic mutations and loss of DAXX protein expression have been frequently found in PanNETs. DAXX is known as a transcriptional repressor, however, molecular functions underlying loss of DAXX remain unclear in PanNETs.

Publication Title

Tumor suppressor functions of DAXX through histone H3.3/H3K9me3 pathway in pancreatic NETs.

Sample Metadata Fields

Treatment

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GSE93595

Acquired resistance with epigenetic alterations under long-term anti-angiogenic therapy for hepatocellular carcinoma

Homo sapiens
4 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Anti-angiogenic therapy is initially effective for several solid tumors including hepatocellular carcinoma (HCC); however, they finally relapse and progress, resulting in poor prognosis. We here established in vivo drug-tolerant subclones of human HCC cells by long-term treatment with vascular endothelial growth factor receptor (VEGFR) inhibitor and serial transplantation in immunocompromised mice (total 12 months), and then compared them with the parental cells in molecular and biological features. Gene expression profiles elucidated a G-actin monomer binding protein thymosin 4 (T4) as one of the genes enriched in the resistant cancer cells relative to the initially sensitive ones. Highlighting epigenetic alterations involved in drug resistance, we revealed that T4 could be aberrantly expressed following demethylation of DNA and active modification of histone H3 at the promoter region. Ectopic overexpression of T4 in HCC cells could significantly enhance sphere-forming capacities and infiltrating phenotypes in vitro, and promote growth of tumors refractory to the VEGFR mutltikinase inhibitor sorafenib in vivo. Clinically, sorafenib failed to improve the progression-free survival in patients with T4-high HCC, indicating that T4 expression could be available as a surrogate marker of susceptibility to this drug. This study suggests that T4 expression triggered by epigenetic alterations could contribute to the development of resistance to anti-angiogenic therapy by the acquisition of stemness, and that epigenetic control might be one of the key targets to regulate the resistance in HCC.

Publication Title

Acquired Resistance with Epigenetic Alterations Under Long-Term Antiangiogenic Therapy for Hepatocellular Carcinoma.

Sample Metadata Fields

Specimen part, Cell line

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SRP064004

Transplantation of gastric organoid-derived spasmolytic polypeptide/TFF2-expressing metaplasia (SPEM) cell lineage promotes ulcer repair in the aged stomach

Mus musculus
10 Downloadable Samples
Illumina HiSeq 1000

Description

Background & Aims: Spasmolytic polypeptide/TFF2-expressing metaplasia (SPEM) is known to emerge following parietal cell loss and during Helicobacter pylori infection, however its role in gastric ulcer repair is unknown. Therefore, we sought to investigate if SPEM plays a role in epithelial regeneration. Methods: Acetic acid ulcers were induced in young (2-3 months) C57BL/6 mice to determine the quality of ulcer repair. Gastric tissue was collected and analyzed to determine the expression of SPEM within the regenerating epithelium. As a comparison to native tissue the expression of SPEM was also identified within cultured gastric mouse-derived organoids. Results: Wound healing in the mice coincided with the emergence of SPEM expressing CD44v within the ulcerated region. The emergence of SPEM was also observed in cultured gastric organoids. Conclusions: These data demonstrate the SPEM may play a role in epithelial regeneration. Conclusions: These data demonstrate the SPEM may play a role in epithelial regeneration. Overall design: 4 samples were used for ulcerated and uninjured tissue. 1 sample was used for intact tissue and organoid-derived RNA. The 'Ulcerated' samples represent C57BL/6 mice with ulcers and the 'Uninjured' samples represent the healthy controls (for "ulcerated" samples). The "Intact stomach tissue" and "Gastric organoids" samples are other types of samples that compared separately. "Gastric organoids" in this comparison are derived from "Intact stomach tissue".

Publication Title

The Development of Spasmolytic Polypeptide/TFF2-Expressing Metaplasia (SPEM) During Gastric Repair Is Absent in the Aged Stomach.

Sample Metadata Fields

Specimen part, Cell line, Subject

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GSE62079

CD73 as a therapeutic target of pancreatic neuroendocrine tumor stem cells

Homo sapiens
2 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Background: Identification and purification of cancer stem cells (CSCs) lead to new therapeutic targets; however, there has been no study to identify and isolated pancreatic neuroendocrine tumor (pNET) CSC. Therefore the clinical significance and its target remain unknown. This study aimed to identify pNET CSCs and characterize therapeutic candidate for pNET CSCs. Methods: We isolated CSCs sorting by ALDH activity in pNET surgical section and cell lines. We verified whether these cells have the property of stemness in vivo and in vitro. Additionally in order to acquire CSC gene profile, genome-wide gene expression profiles were investigated using a microarray technique. Results: ALDHhigh cells, but not control bulk cells, formed spheres, proliferated in hypoxia as well as normoxia and promoted cell motility, which are features of CSCs. Injection of as few as 10 ALDHhigh cells led to subcutaneous tumor formation, and 105 ALDHhigh cells established metastases but not control bulk cells in mice. Comprehensive gene expression analysis revealed that genes associated with mesenchymal stem cell, including CD73, and epithelial-mesenchymal transition (EMT) were overexpressed in ALDHhigh cells. APCP, which is CD73 inhibitor, inhibited sphere formation and cell motility in ALDHhigh cells in vitro, and tumor growth inhibition were observed in ALDHhigh cells in vivo. Conclusions: We identified ALDHhigh cells of pNET and elucidated that they have stemness property. Furthermore we identified CD73 as a target of ALDHhigh cells. CD73 is a promising novel target of pNET CSCs.