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SRP095604
Homo sapiens
8 Downloadable Samples
Illumina HiSeq 2500
Description
We Report the genome-wide RNA expression levels in control and schizophrenia hiPSC dervied NPC treated with neuronal media for 2 days. In total about 15,000 gene expression were detected in all samples, of which 1349 were dysregualted. Overall design: Examination, identification and comparision of mRNA expression profliles in control and schizophrenia npc
Publication Title
Common developmental genome deprogramming in schizophrenia - Role of Integrative Nuclear FGFR1 Signaling (INFS).
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 32 Downloadable Samples
Affymetrix Human Genome U95A Array (hgu95a)
Description
Sarcoidosis + Follow-up 6 month after
Publication Title
Functional genomics and prognosis in sarcoidosis--the critical role of antigen presentation.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 14 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Samples collected from human subjects in clinical trials possess a level of complexity, arising from multiple cell types, that can obfuscate the analysis of data derived from them. Blood, for example, contains many different cell types that are derived from a distinct lineage and carry out a different immunological purpose. Failure to identify, quantify, and incorporate sources of heterogeneity into an analysis can have widespread and detrimental effects on subsequent statistical studies.
Publication Title
Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples.
Sample Metadata Fields
Sex, Specimen part
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
A LysM Receptor-like Kinase Mediates Chitin Perception and Fungal Resistance in Arabidopsis
Publication Title
A LysM receptor-like kinase plays a critical role in chitin signaling and fungal resistance in Arabidopsis.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 19 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Messenger RNA levels in eukaryotes are balanced by two consecutive regulatory layers. Primary, transcriptional regulation at the level of chromatin and secondary, post-transcriptional regulation of the initial transcript in the cytoplasm. Each layer is individually studied in mechanistic detail, while integration of both processes is required to quantify the individual contribution to steady-state RNA levels. Here we show that chromatin features are sufficient to model transcription rate but with different sensitivities in dividing versus post mitotic cells. In both cases chromatin derived transcript levels explains over 80% of variance in measured RNA level enabling to separate transcription from different post-transcriptional processes. By further inclusion of measurements of mRNA half-life and micro RNA expression data we identify a low quantitative contribution of RNA decay by either micro RNA or general differential turnover to final mRNA levels. Together this establishes a chromatin based quantitative model for the contribution of transcriptional and posttranscriptional processes to steady-state levels of messenger RNA.
Publication Title
Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels.
Sample Metadata Fields
Specimen part, Disease, Treatment, Time
View Samples- Rattus norvegicus
- 42 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Tissues are often made up of multiple cell-types. Blood, for example, contains many different cell-types, each with its own functional attributes and molecular signature. In humans, because of its accessibility and immune functionality, blood cells have been used as a source for RNA-based biomarkers for many diseases. Yet, the proportions of any given cell-type in the blood can vary markedly, even between normal individuals. This results in a significant loss of sensitivity in gene expression studies of blood cells and great difficulty in identifying the cellular source of any perturbations. Ideally, one would like to perform differential expression analysis between patient groups for each of the cell-types within a tissue but this is impractical and prohibitively expensive.
Publication Title
Cell type-specific gene expression differences in complex tissues.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Full title: Expression data from whole blood gene expression analysis of stable and acute rejection pediatric kidney transplant patients
Publication Title
Cell type-specific gene expression differences in complex tissues.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 17 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
In blood, the transcription factor C/EBPa is essential for myeloid differentiation and has been implicated in regulating self-renewal of fetal liver hematopoietic stem cells (HSCs). However, its function in adult HSCs is unknown. Here, using an inducible knockout model, we found that C/EBPa deficient adult HSCs underwent a pronounced expansion with enhanced proliferation, characteristics resembling fetal liver HSCs. Consistently, transcription profiling of C/EBPa deficient HSCs revealed a gene expression program similar to fetal liver HSCs. Moreover we observed that age-specific C/EBPa expression correlated with its inhibitory effect on the HSC cell cycle. Mechanistically, we identified N-Myc as a C/EBPa downstream target. C/EBPa upregulation during HSC transition from an active fetal state to a quiescent adult state was accompanied by down-regulation of N-Myc, and loss of C/EBPa resulted in de-repression of NMyc. Our data establish that C/EBPa acts as a molecular switch between fetal and adult states of HSC in part via transcriptional repression of the proto-oncogene N-Myc.
Publication Title
C/EBPa controls acquisition and maintenance of adult haematopoietic stem cell quiescence.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
We report the genome-wide RNA expression levels in pluripotent mESC and as mESC differentiate towards a neuronal lineage in response to high levels of Retinoic Acid treatment in vitro. RNA-seq was performed to identify all RNAs expressed in both ESCs and neuronal cells. In total, In total, 14,443 expressed genes were detected, of which 1,834 were up-regulated and 1,477 down-regulated (fold change (FC) > -/+2.0 and p-value < 0.035) during RA-induced neuronal differentiation. The top down-regulated genes included members of the pluripotency core transcriptional network, including Klf4, Sox2, Oct4, Nanog, Suz12, Esrrb, Stat3 and Tcfcp2l1. The top up-regulated genes are important for neuronal differentiation (e.g. Pax3, Irx3, Rest and Foxd3) and reside in the RA-pathway (e.g. various homeobox genes), the retinoic acid receptors and the RA-degradation enzyme Cyp26a1. Overall design: Examination, identification and comparision of mRNA expression profliles in two cellular states.
Publication Title
Global Developmental Gene Programing Involves a Nuclear Form of Fibroblast Growth Factor Receptor-1 (FGFR1).
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Proteomic analysis of Medulloblastoma reveals functional biology with translational potential.
Sample Metadata Fields
Sex, Specimen part
View Samples