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SRP075613
Homo sapiens
313 Downloadable Samples
Illumina HiSeq 2500
Description
Purpose: Single cell RNA-seq could observe heterogeneity of cell transcriptomes. The goals of this study are to compare the changes of ESCC cell line KYSE-180 RNA profiles in response to different doses of radiotherapy and to analyze the radio-resistance related genes. Overall design: Methods: Cultured KYSE-180 cells accepted accumulative irradiation doses of 0 Gy, 12 Gy or 30 Gy, respectively. Single cell libraries were generated by Smart-seq 2 kit, sequenced using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed at the transcript expression level with TopHat followed by DESeq2/Monocle.
Publication Title
Population and single‑cell transcriptome analyses reveal diverse transcriptional changes associated with radioresistance in esophageal squamous cell carcinoma.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 11 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To identify molecules to serve as diagnostic markers for high-grade prostate cancer (PC) and targets for novel therapeutic drugs, we investigated the gene expression profiles of high-grade PCs using a cDNA microarray combined with laser microbeam microdissection.
Publication Title
The ubiquitin-like molecule interferon-stimulated gene 15 is overexpressed in human prostate cancer.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
The goal of this study was to investigate the role of intragenic CTCF in alternative pre-mRNA splicing through a combined CTCF-ChIP-seq and RNA-seq approach. CTCF depletion led to decreased inclusion of weak upstream exons. Overall design: CTCF ChIP-seq was performed in BJAB and BL41 B cell lines and normalized relative to Rabbit Ig control IP-seq reads. RNA-seq was performed in BJAB and BL41 cells transduced with shRNA against CTCF or RFP as a control, and in untransduced cells as well.
Publication Title
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Cyclic AMP response element binding protein (CREB) is known to play important roles in growth and drug resistance of various cancers. Here we show roles of inhibition of CREB1 on gene expression profile of malignant mesothelioma (MM) cells (Hmeso and H2373/PPMMill).
Publication Title
CREB-induced inflammation is important for malignant mesothelioma growth.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Carbohydrate response element binding protein (ChREBP) is one of the major transcription factors regulating carbohydrate metabolism and lipogenesis.It expresses highly in several tissues including liver, adipose tissue, small intestine,kidney and muscles. Mice with global knockout of ChREBP exhibit intolerance to carbohydrate including glucose and fructose. However, the exact role of liver ChREBP in high carbohydrate stress is not well defined.
Publication Title
Liver ChREBP Protects Against Fructose-Induced Glycogenic Hepatotoxicity by Regulating L-Type Pyruvate Kinase.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Innate immune responses must be regulated in the intestine to prevent excessive inflammation. Here, using gene reporter mice, we show that a subset of mouse colonic macrophages constitutively produced the anti-inflammatory cytokine IL-10. In mice infected with Citrobacter rodentium, which is considered similar to enteropathogenic Escherichia coli infection in humans, macrophage IL-10 was required to prevent intestinal pathology and to promote survival. The synthesis of the proinflammatory cytokine IL-23 was significantly increased in infected mice with a myeloid cell specific deletion of IL-10 and the addition of IL-10 reduced in vitro IL-23 production by intestinal macrophages. Furthermore, blockade of IL-23 led to reduced morbidity and mortality in the context of macrophage IL-10 deficiency. Transcriptome analysis indicated that the reporter positive and negative colonic macrophage subsets were highly similar, but the reporter positive cells differed for the expression of CD163, an IL-10 target gene, suggesting an autocrine IL-10 signal, and when obtained from infected mice, they had reduced IL-23p19 mRNA. Interestingly, only transfer of the reporter positive cells could rescue IL-10 deficient infected mice. Therefore, these data indicate a pivotal role for a subset of intestinal macrophages that constitutively produces IL-10, perhaps acting in part in autocrine fashion, in controlling excessive innate immune activation, regulation of IL-23 production, and prevention of tissue damage after an acute bacterial infection in the intestine.
Publication Title
IL-10-producing intestinal macrophages prevent excessive antibacterial innate immunity by limiting IL-23 synthesis.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Arabidopsis Gene 1.0 ST Array (aragene10st)
Description
Phosphorus is an essential macronutrient element, but some time causes problems if present in excess. Unlike the enormous molecular and morphophysiological information available in plants regarding phosphate (Pi) deficiency, little is known about the effect of excess Pi on plants, which is indeed essential for its remediation. Here, we have carried out a comparative study of plant molecular responses under excess Pi (20 mM) or without Pi (0 mM) at transcriptome level. The 1.25 mM treatment concentration of Pi used as a control to obtain differentially regulated genes under above mentioned Pi regimes. A novel whole-transcript expression array, i.e. Arabidopsis Gene 1.0 ST Array, was used to perform these experiments. The most distinctly regulated groups of genes represent modulation in ethylene mediated signaling, Fe deficiency response, and root development. We have also identified some defensin like genes, possessing a gibberellic acid regulated domain (GASA like) under excess Pi treatment. Overall, this study will not only help in dissecting the mechanism of plant responses under excess Pi but also provide the clues about the unknown genes involved in phosphorus homeostasis.
Publication Title
Comprehensive study of excess phosphate response reveals ethylene mediated signaling that negatively regulates plant growth and development.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Arabidopsis Gene 1.0 ST Array (aragene10st)
Description
Genome-wide transcriptome analysis was carried out in root tissue of Arabidopsis seedlings treated with gold (Au) as Chloroauric acid (HAuCl4). This study demonstrated remarkable changes in root transcriptome within the 12 h exposure. Most of the genes differentially expressed were related to glutathione binding, methylations, secondary metabolism, sugar metabolism, ABA, ethylene, auxin related signalling, transport and signal-transduction pathways.
Publication Title
Genome wide transcriptome analysis reveals ABA mediated response in Arabidopsis during gold (AuCl(-) 4) treatment.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 102 Downloadable Samples
- Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
The specific genes that influence neuroblastoma biology and are targeted by genomic alterations remain largely unknown. We quantified mRNA expression in a highly annotated series of 101 prospectively collected diagnostic neuroblastoma primary tumors and the expression profiles were determined using Affymetrix U95Av2 arrays. Comparisons between the sample groups allow the identification of genes with localized expression patterns. This study demonstrates that the genomic data can be used to subcategorize the disease into molecular subsets and the regional copy number alterations are correlated with a broad number of transcriptional alterations genome wide. This data also suggests that multiple genes from several discrete regions of the human genome co-operate to supress neuroblastoma tumorigenesis and progression.
Publication Title
Integrative genomics identifies distinct molecular classes of neuroblastoma and shows that multiple genes are targeted by regional alterations in DNA copy number.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 24 Downloadable Samples
- IlluminaHiSeq2500
Description
N1-Methyladenosine (m1A) is a prevalent post-transcriptional RNA modification, yet little is known about its abundance, topol- ogy and dynamics in mRNA. Here, we show that m1A is prevalent in Homo sapiens mRNA, which shows an m1A/A ratio of ~0.02%. We develop the m1A-ID-seq technique, based on m1A immunoprecipitation and the inherent ability of m1A to stall reverse tran- scription, as a means for transcriptome-wide m1A profiling. m1A-ID-seq identifies 901 m1A peaks (from 600 genes) in mRNA and noncoding RNA and reveals a prominent feature, enrichment in the 5'' untranslated region of mRNA transcripts, that is dis- tinct from the pattern for N6-methyladenosine, the most abundant internal mammalian mRNA modification. Moreover, m1A in mRNA is reversible by ALKBH3, a known DNA/RNA demethylase. Lastly, we show that m1A methylation responds dynamically to stimuli, and we identify hundreds of stress-induced m1A sites. Collectively, our approaches allow comprehensive analysis of m1A modification and provide tools for functional studies of potential epigenetic regulation via the reversible and dynamic m1A methylation. Overall design: Identification of m1A sites in human embryonic kidney cells. Comparisons of m1A profiles of wild type HEK293T with ALKBH3 knock out cell line reveals the ALKBH3 specific sites. Stress inducible m1A sites are also identified by comparing the profiles of untreated cells with stress treated cells.
Publication Title
Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome.
Sample Metadata Fields
No sample metadata fields
View Samples