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Drosophila melanogaster
12 Downloadable Samples
Illumina Genome Analyzer IIx
Description
To gain insights into the molecular mechanisms underlying the memory consolidation in Drosophila melanogaster, isolated mushroom bodies were subjected to RNA-seq analysis at several time points after a conditioning that induces CREB-dependent olfactory aversive memory.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
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SRP188296- Homo sapiens
- 31 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA-seq involves purification of RNA, followed by either selection of poly-A(+) RNA or depletion of ribosomal RNA. RNA is then converted into cDNA by one of two methods; 1) random priming, followed by cDNA fragmentation, end-repair and Illumina/SOLiD linker ligation or, 2) Enzymatic or chemical RNA fragmentation followed by linker ligation and cDNA generation. Following PCR amplification of tailed cDNA fragments with primers suitable for solid phase (Illumina) or emPCR (SOLiD) clonal amplification RNA-seq libraries are subjected to sequencing. Sequence alignment software is then used to compare the short sequence reads to reference genome and transcriptome databases, and exon-exon junction databases. From this analysis paradigm emerges data that is used for a variety of purposes, including the measurement of gene- level and exon-level expression abundance; detection of base changes (mutations and polymorphisms) relative to reference datasets; measurement of alternative splicing events; identification of gene fusion events; and identification of RNA editing events.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Race
View Samples- Homo sapiens
- 1 Downloadable Sample
Description
Investigate epigenetic mechanisms contributing to stemness/pluripotency in lung cancers and potentially identify novel therapeutic targets in these malignancies.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples E-MTAB-912- Saccharomyces cerevisiae
- 4 Downloadable Samples
Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Administration of spermidine, a natural polyamine whose intracellular concentration declines during human ageing, markedly extends the lifespan of various model organisms including yeast, flies and worms. In ageing yeast, spermidine treatment triggeres epigenetic deacetylation of histone H3 through inhibition of histone acetyltransferases (HAT), leading to induction of autophagy and thereby suppressing oxidative stress and necrosis. In order to further characterize the effects by spermidine supplementation of aging yeast cultures and to understand how global histone deacetylation affects gene transcription during aging, Affymetrix-based microarray analyses of three day old as well as ten day old cultures with and without administration of spermidine was performed.
Publication Title
Induction of autophagy by spermidine promotes longevity.
Sample Metadata Fields
Age, Compound, Time
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
NIH3T3 in the middle of G0 to G1 transion consists of the cells which is still staying G0 phase and the cells which enters G1. Monitoring the expressions of p27 and Cdt1 enables to distinguish these two; p27+/Cdt1+ cells as the cells in G0 phase and p27-Cdt1+ cells as G1 phase
Publication Title
A novel cell-cycle-indicator, mVenus-p27K-, identifies quiescent cells and visualizes G0-G1 transition.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms.
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Classification of Epstein-Barr virus-positive gastric cancers by definition of DNA methylation epigenotypes.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 82 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The aim of this study is to identify responders to FOLFOX therapy by applying the Random Forests (RF) algorithm to gene expression data. Eighty-three unresectable colorectal cancer (CRC) patients including 42 responders and 41 non-responders were divided into training (54 patients) and test (29 patients) sets.
Publication Title
Potential responders to FOLFOX therapy for colorectal cancer by Random Forests analysis.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 66 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
PRC2 overexpression and PRC2-target gene repression relating to poorer prognosis in small cell lung cancer.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 66 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
Small cell lung cancer (SCLC) is a subtype of lung cancer with poor prognosis due to early dissemination and rapid growth. We here analyze gene expression profile of 23 clinical SCLC samples. EZH2 was found to be highly expressed in SCLC samples compared to 42 normal tissues including the normal lung, and other PRC2 members, SUZ12 and EED, were also highly expressed in SCLC. To obtain target genes of PRC2 in SCLC, H3K27me3 mark was mapped in three SCLC cell lines, Lu130, H209 and DMS53, and compared to normal small airway epithelial cells (SAEC). Whereas H3K27me3(+) genes in SAEC were significantly overlapped with PRC-target genes in ES cells (P=1.7x10-31), genes with H3K27me3 in SCLC cell lines but not in SAEC were not significantly overlapped with PRC-target genes in ES cells (P=0.64). These genes with H3K27me3 specifically in SCLC cell lines but not in SAEC showed decreased expression, not only in SCLC cell lines but also in clinical SCLCs, and showed enrichment of GO-terms such as plasma membrane (P=8.1x10-21) and cell adhesion (P=1.7x10-8). Introduction of JUB, a gene showing specific H3K27me3 modification and the strongest repression in the three SCLC cell lines, resulted in repression of cellular growth in DMS53. In clinical SCLC cases, lower JUB level correlated to shorter survival (P=0.002), or a set of PRC target genes (JUB, EPHB4) and marker genes of classic type SCLC (GRP, ASCL1) correlated to shorter survival (P=0.0001) and classified SCLC into two groups with distinct prognosis. Growth of SCLC cell lines was repressed when treated with 3-Deazaneplanocin A, an inhibitor against PRC2. It is suggested that high expression of PRC2 in SCLC contributed to repression of genes including non-PRC-target genes in ES cells, and that the gene repression may play a role in genesis of SCLC.
Publication Title
PRC2 overexpression and PRC2-target gene repression relating to poorer prognosis in small cell lung cancer.
Sample Metadata Fields
Specimen part, Cell line
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