submitter_institution:Joan Steitz Results

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Microarray (39)

Rna-seq (7)

Platform

Affymetrix Mouse Gene 2.1 ST Array (mogene21st) (30)

Affymetrix Human Gene 2.1 ST Array (hugene21st) (30)

Affymetrix Human Genome U219 Array (hgu219) (23)

Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) (23)

Illumina HiSeq 2000 (1)

Includes Publication (6)

SRP058633

Homo sapiens Raw sequence reads

Homo sapiens
6 Downloadable Samples

Description

This study identified genomwide KCl inducible readthrough transcription. The project also includes a Cap-Seq experiment to identify transcriptional start sites, demonstrating that KCl does not activate downstream transcriptional start sites, but indeed does induce readthrough

Publication Title

Widespread Inducible Transcription Downstream of Human Genes.

Sample Metadata Fields

No sample metadata fields

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SRP073410

NIH3T3 RNA-Seq after stress

Mus musculus
1 Downloadable Sample
Illumina HiSeq 2000

Description

Illumina RNA-Seq of the nuclear RNA fraction (total RNA, no poly(A) selection from NIH3T3 cells treated with heat shock, osmotic stress, or oxidative stress

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part, Treatment

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GSE54721

DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma.

Homo sapiens
23 Downloadable Samples
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482), Affymetrix Human Genome U219 Array (hgu219)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

DNA methylation fingerprint of neuroblastoma reveals new biological and clinical insights.

Sample Metadata Fields

Specimen part

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GSE73509

CaSR modulator in neuroblastoma model

Mus musculus, Homo sapiens
30 Downloadable Samples
Affymetrix Mouse Gene 2.1 ST Array (mogene21st), Affymetrix Human Gene 2.1 ST Array (hugene21st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Cinacalcet inhibits neuroblastoma tumor growth and upregulates cancer-testis antigens.

Sample Metadata Fields

Specimen part, Treatment

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GSE54720

DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma [gene expression]

Homo sapiens
23 Downloadable Samples
Affymetrix Human Genome U219 Array (hgu219)

Description

DNA methylation changes in neuroblastoma, a clinically-heterogeneous pediatric tumor, have been described essentially in promoter regions. We analyzed the DNA methylome of neuroblastoma using high-density microarrays and observed differential methylation not only in promoters but also in intragenic and intergenic regions at both CpG and non-CpG sites. These epigenetic changes showed a non-random distribution relative functional chromatin domains, and targeted development and cancer-related genes, relevant for neuroblastoma pathogenesis. CCND1, a gene overexpressed in neuroblastoma, showed hypomethylation of gene-body and upstream regulatory regions. Furthermore, tumors with diverse clinical-risk showed clear differences affecting CpG and, remarkably, non-CpG sites. Non-CpG methylation was present in clinically-favorable tumors and affected genes such as ALK, where non-CpG methylation correlated with low gene expression. Finally, we identified CpG and non-CpG methylation signatures which correlated with patients age at time-points relevant for neuroblastoma clinical behavior, and targeted genes related to neural development and neural crest regulatory network