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Homo sapiens
16 Downloadable Samples
Affymetrix Human Gene Expression Array (primeview), Illumina HumanHT-12 V4.0 expression beadchip, Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the United States Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for sequence discovery and differential expression profiling and compare it to microarray and quantitative PCR (qPCR) data using complementary metrics. At all sequencing depths, we discover unannotated exon-exon junctions, with >80% validated by qPCR. We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific filters are used. In contrast, RNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed, for these and qPCR. Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcriptlevel profiling. The complete SEQC data sets, comprising >100 billion reads (10Tb), provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings.
Publication Title
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 638 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Gene-expression microarray datasets generated as part of the Immunological Genome Project (ImmGen). Primary cells from multiple immune lineages are isolated ex-vivo, primarily from young adult B6 male mice, and double-sorted to >99% purity. RNA is extracted from cells in a centralized manner, amplified and hybridized to Affymetrix 1.0 ST MuGene arrays. Protocols are rigorously standardized for all sorting and RNA preparation. Data is released monthly in batches of cell populations.
Publication Title
Transcriptomes of the B and T lineages compared by multiplatform microarray profiling.
Alternate Accession IDs
Sample Metadata Fields
Sex, Age
View Samples- Homo sapiens
- 233 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Two gene co-expression modules differentiate psychotics and controls.
Alternate Accession IDs
Sample Metadata Fields
Sex, Age, Specimen part, Disease
View Samples- Homo sapiens
- 123 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Schizophrenia (SCZ) and bipolar disorder (BD) are highly heritable psychiatric disorders. Associated genetic and gene expression
Publication Title
Two gene co-expression modules differentiate psychotics and controls.
Alternate Accession IDs
Sample Metadata Fields
Sex, Age, Specimen part, Disease
View Samples- Homo sapiens
- 110 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Schizophrenia (SCZ) and bipolar disorder (BD) are highly heritable psychiatric disorders. Associated genetic and gene expression
Publication Title
Two gene co-expression modules differentiate psychotics and controls.
Alternate Accession IDs
Sample Metadata Fields
Sex, Age, Specimen part, Disease
View Samples- Mus musculus, Homo sapiens
- 38 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Identification of evolutionarily conserved gene networks mediating neurodegenerative dementia.
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Homo sapiens
- 35 Downloadable Samples
Description
Purpose: The goal of this study was to assess gene expression changes upon SAHA treatment in neurons derived from patients with A152T Tau mutation Overall design: iPSC derived neurons were treated with SAHA at different dosage for several days
Publication Title
Identification of evolutionarily conserved gene networks mediating neurodegenerative dementia.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 35 Downloadable Samples
- Illumina HiSeq 4000
Description
Purpose: The goal of this study was to assess gene expression changes upon SAHA treatment in cells overexpressing miR-203. Overall design: Primary cortical cultures were established using E15 cortical cultures from C57BL/6J mice. At DIV0, cells were infectd with either miR-203 (high titre - 1MOI) or intermediate titre (0.5MOI) or control (high 1MOI) lentivirus andalso treated with different dose of SAHA. At DIV8, total RNA was isolated using NucleoSpin RNA XS kit (Takara). Libraries were prepared using Standard illumina stranded mRNA-seq protocol.
Publication Title
Identification of evolutionarily conserved gene networks mediating neurodegenerative dementia.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Subject
View Samples
GSE75306- Mus musculus
- 154 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Parsing the Interferon Transcriptional Network and Its Disease Associations.
Alternate Accession IDs
Sample Metadata Fields
Sex, Age, Specimen part, Treatment, Time
View Samples- Mus musculus
- 26 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
We analyze the expression profile of ISGs in the context of IFNAR1-KO primary murine B cells and macrophages. These analses were used to define ISG gene sets that are under tonic control. Furthermore, these analyses enabled the definition of ISGs that are dependent on Tyk2 signaling.
Publication Title
Parsing the Interferon Transcriptional Network and Its Disease Associations.
Alternate Accession IDs
Sample Metadata Fields
Sex, Age
View Samples