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Mus musculus
9 Downloadable Samples
Illumina HiSeq 2000
Description
We profiled total liver mRNA of WT and p21KO mice that were fed ad libitum or fasted for 24 hours Overall design: 2-3 mice of each genotype were either fed or fasted for 24 hours, sacrificed and total mRNA was extracted from liver (we mapped >12M reads per sample)
Publication Title
p21<sup>Cip1</sup> plays a critical role in the physiological adaptation to fasting through activation of PPARα.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 25 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
The goal was to identify the differently expressed genes between laryngeal tumor and nonmalignant surrounding mucosa
Publication Title
Transcriptome Analysis Identifies ALCAM Overexpression as a Prognosis Biomarker in Laryngeal Squamous Cell Carcinoma.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Subject
View Samples- Saccharomyces cerevisiae
- 14 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Sir2 is an NAD+-dependent histone deacetylase, and is the founding member of a large, phylogentically conserved, family of such deacetylases called the Sirtuins. The budding yeast, Saccharomyces cerevisiae, harbors 4 paralogs of Sir2, known as Hst1, Hst2, Hst3, and Hst4. Reducing the intracellular NAD+ concentration is inhibitory for the Sirtuins, and raising the intracellular nicotinamide (NAM) concentration is inhibitory. Microarray gene expression analysis was used to identify novel classes of yeast genes whose expression is altered when either NAD+ concentration is reduced or NAM is elevated. A subset of genes involved in thiamine biosynthesis was identified as being upregulated when Sir2 or Hst1 was inactivated.
Publication Title
Thiamine biosynthesis in Saccharomyces cerevisiae is regulated by the NAD+-dependent histone deacetylase Hst1.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 10 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
The chronological lifespan (CLS) of Saccharomyces cerevisiae is defined as the number days that non-dividing cells remain viable, typically in stationary phase cultures or in water. CLS is extended by restricting glucose in the starting cultures, and is considered a form of caloric restriction (CR). Through a previous genetic screen our lab determined that deleting components of the de novo purine biosynthesis pathway also significantly increased CLS. Significant similarities in gene expression profiles between calorie restricted WT cells and a non-restricted ade4 mutant suggested the possibility of common gene expression biomarkers of all chronologically long lived cells that could also provide insights into general mechanisms of lifespan extension. We have identified additional growth conditions that extend CLS of WT cells, including supplementation of the media with isonicotinamide (INAM), a known sirtuin activator, or by supplementation with a concentrate collected from the expired media of a calorie restricted yeast culture, presumably due to an as yet unidentified longevity factor. Using these varied methods to extend CLS, we compared gene expression profiles in the aging cells (at day 8) to identify functionally relevant biomarkers of longevity. Nineteen genes were differentially regulated in all 4 of the long-lived populations relative to wild type. Of these 19 genes, viable haploid deletion mutants were available for 16 of them, and 12 were found to have a significant impact on CLS.
Publication Title
Functional genomic analysis reveals overlapping and distinct features of chronologically long-lived yeast populations.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 909 Downloadable Samples
- Illumina HiSeq 2000
Description
Identification of blood biomarkers that prospectively predict Mycobacterium tuberculosis treatment response. Overall design: There are a total of 914 samples used in this design. This involves samples from 100 cases and 38 controls. Most of the samples have 2 technical replicates where as 2 samples have 4. Samples from the TB cases have been collected on the start day of TB treatment and on 1,4 and 24 weeks after treatment as well. For some subjects we also have samples after the subject has been cured. The case or TB Subjects have been categorized by the nature of their response as definite,probable or possible cure. The day of cure is presented in the time to negativity column. Also provided in the metadata are the MGIT -Mycobacteria Growth Indicator Tube and XPERT (cartridge based nucleic acid amplification test, automated diagnostic test that can identify Mycobacterium tuberculosis (MTB)) values at the various times of sample collection for all TB Subjects.
Publication Title
Host blood RNA signatures predict the outcome of tuberculosis treatment.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Subject, Time
View Samples
GSE74321- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Comparison of gene expression in intestinal epithelial cells in the presence or absence of ectopic induction of Msi1 in vivo
Publication Title
The Msi Family of RNA-Binding Proteins Function Redundantly as Intestinal Oncoproteins.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 94 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
hTERT/cdk4 immortalized myogenic human cell lines represent an important tool for skeletal muscle research, being used as therapeutically-pertinent models of various neuromuscular disorders and in numerous fundamental studies of muscle cell function. However, the cell cycle is linked to other cellular processes such as integrin regulation, the PI3K/Akt pathway, and microtubule stability, raising the question as to whether transgenic modification of the cell cycle results in secondary effects that could undermine the validity of these cell models. Here we subjected healthy and disease lines to intensive transcriptomic analysis, comparing immortalized lines with their parent primary populations in both differentiated and undifferentiated states, and testing their myogenic character by comparison with non-myogenic (CD56-negative) cells. We found that immortalization has no measurable effect on the myogenic cascade or on any other cellular processes, and that it was protective against the systems level effects of senescence that are observed at higher division counts of primary cells.
Publication Title
Skeletal muscle characteristics are preserved in hTERT/cdk4 human myogenic cell lines.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 71 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Acute Lymphoblastic Leukemia (ALL) in infants (<1 year) is characterized by a poor prognosis and a high incidence of MLL translocations. Several studies demonstrated the unique gene expression profile associated with MLL-rearranged ALL, but generally small cohorts were analyzed as uniform patient groups regardless of the type of MLL translocation, while the analysis of translocation-negative infant ALL remained unacknowledged.
Publication Title
Gene expression profiling-based dissection of MLL translocated and MLL germline acute lymphoblastic leukemia in infants.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 52 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Although the prognosis for childhood Acute Lymphoblastic Leukemia (ALL) in general has improved tremendously over the last decades, the survival chances for infants (<1 year of age) with ALL remains poor.
Publication Title
Association of high-level MCL-1 expression with in vitro and in vivo prednisone resistance in MLL-rearranged infant acute lymphoblastic leukemia.
Sample Metadata Fields
Sex, Specimen part, Disease
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We studied the KRAS and NRAS mutational status in pediatric MLL-AF4+ leukemia patients by means of ultra deep amplicon sequencing. The gene expression profiles of RAS wild type and RAS mutated patients were investigated by gene expression analysis. We showed that mutated patients were characterized by a RAS related expression signature.
Publication Title
Deciphering KRAS and NRAS mutated clone dynamics in MLL-AF4 paediatric leukaemia by ultra deep sequencing analysis.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Subject
View Samples