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Homo sapiens
59 Downloadable Samples
Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Optic neuritis (ON) is a common manifestation of multiple sclerosis (MS); it appears as the presenting symptom in about 25% of MS patients and occurs in 3070% of patients with MS during the course of their illness
Publication Title
The role of B cells in the early onset of the first demyelinating event of acute optic neuritis.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 10 Downloadable Samples
IlluminaHiSeq2500
Description
The human nuclear poly(A)-binding protein PABPN1 has been implicated in the decay of nuclear noncoding RNAs (ncRNAs). In addition, PABPN1 stimulates hyperadenylation by poly(A) polymerase, and this activity is thought to be required for decay. Here, we inactivated hyperadenylation by two distinct mechanisms and examined changes in gene expression in HEK293 cells by RNAseq. We observed the upregulation of various ncRNAs, including snoRNA host genes, primary miRNA transcripts, and upstream antisense RNAs, confirming that hyperadenylation is broadly required for the degradation of PABPN1-targets. In addition, we found that mRNAs with retained introns are susceptible to PABPN1 and PAPa/?-mediated decay (PPD). Transcripts are targeted for degradation due to inefficient export, which is a consequence of reduced intron number or incomplete splicing. We conclude that PPD is an important mammalian nuclear RNA decay pathway for the removal of poorly spliced and nuclear-retained transcripts. Overall design: Poly(A)+ RNA from HEK293 cells was analyzed by next generation sequencing following depletion of PAPa and PAP? or expression of a dominant negative allele of PABPN1 (LALA) designed to inhibit polyadenylation. For each condition, we collected both total RNA and a nuclear-enriched sample. Each sample was collected in duplicate.
Publication Title
Canonical Poly(A) Polymerase Activity Promotes the Decay of a Wide Variety of Mammalian Nuclear RNAs.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 117 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
Background: Gene expression profiling has shown its ability to identify with high accuracy low cytogenetic risk acute myeloid leukemia such as acute promyelocytic leukemia and leukemias with t(8;21) or inv(16). The aim of this gene expression profiling study was to evaluate to what extent suboptimal samples with low leukemic blast load (range, 2-59%) and/or poor quality control criteria could also be correctly identified. Methods: Specific signatures were first defined so that all 71 acute promyelocytic leukemia, leukemia with t(8;21) or inv(16)-AML as well as cytogenetically normal acute myeloid leukemia samples with at least 60% blasts and good quality control criteria were correctly classified (training set). The classifiers were then evaluated for their ability to assign to the expected class 111 samples considered as suboptimal because of a low leukemic blast load (n=101) and/or poor quality control criteria (n=10) (test set). Results: With 10-marker classifiers, all training set samples as well as 97 of the 101 test samples with a low blast load, and all 10 samples with poor quality control criteria were correctly classified. Regarding test set samples, the overall error rate of the class prediction was below 4 percent, even though the leukemic blast load was as low as 2%. Sensitivity, specificity, negative and positive predictive values of the class assignments ranged from 91% to 100%. Of note, for acute promyelocytic leukemia and leukemias with t(8;21) or inv(16), the confidence level of the class assignment was influenced by the leukemic blast load. Conclusion: Gene expression profiling and a supervised method requiring 10-marker classifiers enable the identification of favorable cytogenetic risk acute myeloid leukemia even when samples contain low leukemic blast loads or display poor quality control criterion.
Publication Title
Routine use of microarray-based gene expression profiling to identify patients with low cytogenetic risk acute myeloid leukemia: accurate results can be obtained even with suboptimal samples.
Sample Metadata Fields
Time
View Samples- Homo sapiens
- 27 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Routine use of microarray-based gene expression profiling to identify patients with low cytogenetic risk acute myeloid leukemia: accurate results can be obtained even with suboptimal samples.
Sample Metadata Fields
Specimen part, Time
View Samples- Homo sapiens
- 71 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Endometrial cancer is one of the most common gynecologic malignancies, and patients with high grade disease, especially serous papillary subtype (SPEC) are often related to the poor outcomes. Recent genome-wide analyses have revealed that SPEC exhibits gene expression profiles that are distinct from the endometrioid histologic subtype; therefore, it is important to identify the SPEC driver genes or pathways responsible for the inherently aggressive phenotypes and to develop SPEC-specific therapies to target these driver genes or pathways.
Publication Title
STAT1 drives tumor progression in serous papillary endometrial cancer.
Sample Metadata Fields
Specimen part, Cell line
View Samples
GSE5513- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Polyethylene glycol sorbitan monoacylates (Tween) are detergents of widespread use in plant sciences. We show them, notably Tween 20, to cause a rapid and complex change in transcript abundance which bears all characteristics of a PAMP / elicitor-induced defense response, and they do so at concentrations which cause no detectable deleterious effects on plant cellular integrity. The activity does not reside in the intact Tween molecule itself, but is caused by medium-chain fatty acids, notably lauric acid (LA), which are efficiently released from the Tween-backbone by the plant. The Tween / LA-response is independent of the jasmonate signalling system. Medium-chain fatty acids are thus novel elicitors/regulators of plant pathogen defense. The results also have several practical implications: (i) The use of Tweens and, as we show, several other detergents, as solvating/wetting agents on intact plants causes profound physiological changes which may mask actual effects of test compounds; (ii) Tweens by themselves can be regarded (and probably used) as economical, non-toxic, and safe-to-apply elicitors of inducible plant immunity against pathogens.
Publication Title
A novel regulatory system in plants involving medium-chain fatty acids.
Sample Metadata Fields
Age
View Samples- Homo sapiens
- 48 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA was purified cancer cell lines. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech's ExpressionPlot database is PRJ0013114 Overall design: RNA from NSCLC cell lines after treatment with either DMSO, GDC-0973, AZ-628 or the combination of AZ-628 and GDC-0973 all at 0.1 micro-molar concentration.
Publication Title
Pharmacological Induction of RAS-GTP Confers RAF Inhibitor Sensitivity in KRAS Mutant Tumors.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Cerebral malaria (CM) can be a fatal manifestation of Plasmodium falciparum infection. We examined global gene expression patterns by microarray during fatal murine CM (FMCM) and non-cerebral malaria (NCM). There was differential expression of a number of genes, including some not yet characterized in the pathogenesis of FMCM. Some gene induction was observed during Plasmodium infection regardless of the development of CM and there was a predominance of genes linked to IFN responses, even in NCM. However, upon real-time PCR validation and quantitation, these genes were much more highly expressed in FMCM than in NCM. The observed changes included genes belonging to pathways such as interferon (IFN) signaling, MHC processing and presentation, apoptosis, immunomodulatory and anti-microbial processes. We further characterized differentially expressed genes by examining the cellular source of their expression as well as their temporal expression patterns during the course of malaria infection. These data identify a number of novel genes that represent interesting candidates for further investigation in FMCM.
Publication Title
Predominance of interferon-related responses in the brain during murine malaria, as identified by microarray analysis.
Sample Metadata Fields
Sex, Specimen part, Disease
View Samples- Mus musculus
- 16 Downloadable Samples
- Illumina HiSeq 2500
Description
The RING domain protein Arkadia/RNF111 is a ubiquitin ligase in the transforming growth factor beta (TGFß) pathway. We previously identified Arkadia as a small ubiquitin-like modifier (SUMO)-binding protein with clustered SUMO-interacting motifs (SIMs) that together form a SUMO-binding domain (SBD). However, precisely how SUMO interaction contributes to the function of Arkadia was not resolved. Through analytical molecular and cell biology, we found that the SIMs share redundant function with Arkadia''s M domain, a region distinguishing Arkadia from its paralogs ARKL1/ARKL2 and the prototypical SUMO-targeted ubiquitin ligase (STUbL) RNF4. The SIMs and M domain together promote both Arkadia''s colocalization with CBX4/Pc2, a component of Polycomb bodies, and the activation of a TGFbeta pathway transcription reporter. Transcriptome profiling through RNA sequencing showed that Arkadia can both promote and inhibit gene expression, indicating that Arkadia''s activity in transcriptional control may depend on the epigenetic context, defined by Polycomb repressive complexes and DNA methylation [Sun, Liu, and Hunter (2014) Mol Cell Biol 34(16):2981-2995]. Overall design: To determine the role of Arkadia in TGFß signaling at the transcriptome level, the profiles of TGFß-stimulated gene expression were examined in Ark+/+ (Ark_WT), Ark-/- (Ark_null), and Arkadia (WT and sim mutant)-reconstituted Ark-/- MEFs. RNA sequencing was carried out using poly(A)-enriched RNA samples from unstimulated cells and cells treated with TGFß for 1h, 4h, or 16h as indicated. Two batches of sequencing data for a total of 16 independent samples were submitted.
Publication Title
Multiple Arkadia/RNF111 structures coordinate its Polycomb body association and transcriptional control.
Sample Metadata Fields
No sample metadata fields
View Samples- Gallus gallus
- 6 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
The differentiation and proliferation of chicken B cells rely on the antigens on the cell surface of bursal stromal cells. Chicken stem cell antigen 2 (SCA2) is localized on the surface of bursal cortical and medullary epithelial cells. The signals through SCA2 may regulate the expressions critical for the B cell development.
Publication Title
Cloning and functional characterization of chicken stem cell antigen 2.
Sample Metadata Fields
Specimen part
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