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SRP069839
Danio rerio
16 Downloadable Samples
IlluminaHiSeq2500
Description
We use the zebrafish embryo model to study the innate immune response against polystyrene particles. Therefore, we injected 700nm polystyrene into the yolk at 2 dpf and took samples at 1 and 3 days post injection. Overall design: This deep sequence study was designed to determine the gene expression profile by polystyrene particle toxicity. RNA was isolated from embryos at 1 and 3 days post injection. Wildtypes zebrafish embryos were micro-injected into the yolk (2dpf) with 1nl of 5mg/ml of 700nm red fluorescent polystyrene particles suspended in PVP (Polyvinylpyrrolidone) (n=3), mock injected with pvp (n=2), or Non-injected as a control (n=3). After injections embryos were transferred into fresh egg water and incubated at 28°C. At 1 and 3 days post injection 10 embryos per group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.
Publication Title
Pathway analysis of systemic transcriptome responses to injected polystyrene particles in zebrafish larvae.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Cell type specific transcriptome analysis from laser microdissected megaspore mother cells (MMC) from Arabidopsis thaliana (L.) Heynh., accession Landsberg erecta.
Publication Title
Transcriptome analysis of the Arabidopsis megaspore mother cell uncovers the importance of RNA helicases for plant germline development.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Nucellus tissue surrounding the megaspore mother cell in Arabidopsis thaliana (L.) Heynh. , accession Landsberg erecta, isolated by laser assisted microdissection
Publication Title
Transcriptome analysis of the Arabidopsis megaspore mother cell uncovers the importance of RNA helicases for plant germline development.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 203 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Brain metastasis is one of the most feared complications of cancer and the most common intracranial malignancy in adults. Its underlying mechanisms remain unknown. From breast cancer patients with metastatic disease we isolated cell populations that aggressively colonize the brain. Transcriptomic analysis of these cells yielded overlapping gene sets whose expression is selectively associated with brain metastasis. The expression of seventeen of these genes in primary breast tumors is associated with brain relapse in breast cancer patients. Some of these genes are also associated with metastasis to lung but not to liver, bone or lymph nodes, providing a molecular basis for the long-observed link between brain and lung metastasis. Among the functionally validated brain metastasis genes, the cyclooxigenase COX-2, the EGFR ligand HB-EGF, and the brain-specific 2-6 sialyltransferase ST6GALNAC5 mediate cancer cell passage through the blood-brain barrier. Other brain metastasis genes encode inflammatory factors and brain-specific proteolytic regulators, suggesting a multifaceted program for breast cancer colonization of the brain.
Publication Title
Genes that mediate breast cancer metastasis to the brain.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 13 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Brain metastasis is one of the most feared complications of cancer and the most common intracranial malignancy in adults. Its underlying mechanisms remain unknown.
Publication Title
Genes that mediate breast cancer metastasis to the brain.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 57 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Validation of lung metastasis signature (LMS) and its association with risk of developing lung metastasis and with primary tumor size.
Publication Title
Lung metastasis genes couple breast tumor size and metastatic spread.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
We previously identified a novel SNF1/AMPK-related protein kinase, Hunk, from a mammary tumor arising in an MMTV-neu transgenic mouse. The function of this kinase is unknown. Using targeted deletion in mice, we now demonstrate that Hunk is required for the metastasis of c-myc-induced mammary tumors, but is dispensable for normal development. Reconstitution experiments revealed that Hunk is sufficient to restore the metastatic potential of Hunk-deficient tumor cells, as well as defects in migration and invasion, and does so in a manner that requires its kinase activity. Consistent with a role for Hunk in the progression of human cancers, the human homologue of Hunk is overexpressed in aggressive subsets of carcinomas of the ovary, colon, and breast. In addition, a murine gene expression signature that distinguishes Hunk-wild type from Hunk-deficient mammary tumors predicts clinical outcome in women with breast cancer. Together, these findings establish a role for Hunk in metastasis and an in vivo function for this kinase.
Publication Title
The Snf1-related kinase, Hunk, is essential for mammary tumor metastasis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 206 Downloadable Samples
- IlluminaGenomeAnalyzerIIx
Description
No description.
Publication Title
MicroRNA sequence and expression analysis in breast tumors by deep sequencing.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 185 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Background: Histologic grade in breast cancer provides clinically important prognostic information. However, 30%-60% of tumors are classified as histologic grade 2. This grade is associated with an intermediate risk of recurrence and is thus not informative for clinical decision making. We examined whether histologic grade was associated with gene expression profi les of breast cancers and whether such profi les could be used to improve histologic grading.
Publication Title
Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis.
Sample Metadata Fields
Age, Disease stage
View Samples- Homo sapiens
- 100 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Methylation of cancer-stem-cell-associated Wnt target genes predicts poor prognosis in colorectal cancer patients.
Sample Metadata Fields
Sex, Age, Specimen part, Disease
View Samples