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GSE14645
Mus musculus
9 Downloadable Samples
Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
Folate-mediated one-carbon metabolism is required for purine, thymidylate, and S-adenosylmethionine synthesis. Impairments in folate metabolism diminish cellular methylation potential and genome stability. Cytoplasmic serine hydroxymethyl transferase (cSHMT) regulates partitioning between thymidylate and SAM biosynthesis. These experiments were designed to determine if mutations in cSHMT led to alterations in gene expression.
Publication Title
Shmt1 heterozygosity impairs folate-dependent thymidylate synthesis capacity and modifies risk of Apc(min)-mediated intestinal cancer risk.
Sample Metadata Fields
Age
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
The metabolic pathways that underlie the association between folate deficiency and increased risk for colorectal cancer (CRC) remain unclear. We have studied the effect of C1THF synthase (encoded by the Mthfd1 gene) and dietary folate and choline on intestinal tumor development in Apcmin/+ mice and azoxymethane (AOM)-induced colon cancer in mice. Mthfd1 deficiency did not alter tumor number or load in Apcmin/+ mice, but did result in a decreased incidence of colon tumors. Conversely, Mthfd1 deficiency increased tumor number 3.5-fold and tumor load 2-fold in AOM-treated mice. Here we tested colons isolated from wildtype and Mthfd1-deficient animals for alterations in gene expression.
Publication Title
Mthfd1 is a modifier of chemically induced intestinal carcinogenesis.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 55 Downloadable Samples
Illumina Genome Analyzer IIx
Description
Daily sampling of peripheral blood from human subjects vaccinated for influenza was done immediately before vaccination and for 10 days after vaccination. In B cells, 90% of transcriptomic variation in subjects who received influenza vaccine within the previous three years was explained by a single temporal pattern unique to the individual. A common set of 742 genes was strongly correlated with the migration of differentiating plasma cell subtypes. Overall design: Five subjects, 11 time points per subject (pre-vaccination and daily for 10 days post-vaccination)
Publication Title
High-resolution temporal response patterns to influenza vaccine reveal a distinct human plasma cell gene signature.
Sample Metadata Fields
Specimen part, Subject, Time
View Samples- Homo sapiens
- 55 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
Daily sampling of peripheral blood from human subjects vaccinated for influenza was done immediately before vaccination and for 10 days after vaccination. Temporal patterns of gene expression, determined by RNA-seq, in unfractionated PBMC suggested migration of myeloid/dendritic cell lineage cells one day after vaccination. Overall design: Five subjects, 11 time points per subject (pre-vaccination and daily for 10 days post-vaccination)
Publication Title
High-resolution temporal response patterns to influenza vaccine reveal a distinct human plasma cell gene signature.
Sample Metadata Fields
Specimen part, Subject, Time
View Samples- Mus musculus
- 9 Downloadable Samples
- Illumina HiSeq 2500
Description
Sequencing of RNA isolated from the tibialis anterior muscles of 6 month old C57BL/6J mice that had been injected and electroporated with either a control non-targeting siRNA (NT) or two different UBR4 targeting siRNA sequences (UBR4 siRNA5 and siRNA7) to deplete UBR4. Muscles were harvested 7 days after electroporation and showed significant loss of UBR4 coincident with hypertrophy of type 2A and 2X myofibers. Overall design: 3 samples each of non targeting control and 2 siRNA UBR4 targeting constructs.
Publication Title
A Key Role for the Ubiquitin Ligase UBR4 in Myofiber Hypertrophy in Drosophila and Mice.
Sample Metadata Fields
Age, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 36 Downloadable Samples
- Illumina HiSeq 2500
Description
We report the gene expression profiles of normal epithelial and carcinoma cell populations that differ in their relative levels of integrin-beta 4 expression. ITGB4 high, mesenchymal subtype, triple-negative breast cancer cells were found to be more epithelial than related ITGB4 low cells. Overall design: RNA-seq was used to compare the expression of mesenchymal-like carcinoma cell subtypes isolated from polyclonal cell populations. Isolated cell populations that had high levels of ITGB4 were found to be more epithelial than those with low levels, despite the fact that they were within the mesenchymal-like cell state spectrum.
Publication Title
Integrin-β4 identifies cancer stem cell-enriched populations of partially mesenchymal carcinoma cells.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Respiratory innate immunity requires alveolar macrophages, which are specifically targeted by the S. aureus toxin alpha toxin. These data compare the response of alveolar macrophages to S. aureus with or without alpha toxin neutralization.
Publication Title
S. aureus Evades Macrophage Killing through NLRP3-Dependent Effects on Mitochondrial Trafficking.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Homo sapiens
- 10 Downloadable Samples
- Ion Torrent Proton
Description
To gain insights into tumor heterogeneity in anti-cancer drug responses of patient-derived xenograft models of HER2+ breast cancer brain metastases, we performed transcriptome gene expression profiling by Ion AmpliSeqâ„¢ Transcriptome sequencing that targets more than 20,000 human genes. Our data found that all anti-cancer drugs responders have significantly higher expression levels of AKT-mTOR-dependent signature genes as compared to the non-responders, suggesting that most HER2+ breast cancer brain metastases are depend on the AKT-mTOR pathway Overall design: Gene expression profiles of five PDX samples were generated by Ion AmpliSeq Transcriptome sequencing, in duplcate, using Ion torrent Proton machine.
Publication Title
Combination inhibition of PI3K and mTORC1 yields durable remissions in mice bearing orthotopic patient-derived xenografts of HER2-positive breast cancer brain metastases.
Sample Metadata Fields
Specimen part, Disease, Subject
View Samples- Homo sapiens
- 7 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
ARC (NSC 188491, SMA-491), 4-amino-6-hydrazino-7-beta-d-ribofuranosyl-7H-pyrrolo-(2,3-d)-pyrimidine-5-carboxamide, is a nucleoside analog with profound in vitro anti-cancer activity. First identified in a high-throughput screen for inhibitors of p21 mRNA expression, subsequent experiments showed that ARC also repressed expression of hdm2 and survivin, leading to its classification as a global inhibitor of transcription 1. The following Hu U133 plus 2.0 arrays represent single time point (24 hour) gene expression analysis of transcripts altered by ARC treatment. Arrays for the other compounds (sangivamycin and doxorubicin) are included as comparators.
Publication Title
ARC (NSC 188491) has identical activity to Sangivamycin (NSC 65346) including inhibition of both P-TEFb and PKC.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U219 Array (hgu219)
Description
As a transcription factor, SOX7 suppresses cancer development. However, only a few genes were demonstrated as SOX7-activated targets in cancer-irrelevant contexts. We used microarray chips to determine SOX7 target genes in breast cancer cells and discovered multiple signaling pathways altered by ectopic SOX7. We also investigated several genes for their roles in SOX7-mediated tumor suppression. Our study innovatively revealed SOX7 target gene profile in a cancer-relevant context and identified several SOX7-repressed target genes.
Publication Title
SOX7 Target Genes and Their Contribution to Its Tumor Suppressive Function.
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples