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SRP044781
Danio rerio
12 Downloadable Samples
IlluminaHiSeq2000
Description
Transcriptome analysis of 12 zebrafish tissues
Publication Title
Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 21 Downloadable Samples
Affymetrix Rat Expression 230A Array (rae230a)
Description
Modulation of several waves of gene expression during FGF-1 induced Epithelial-mesenchymal transition of carcinoma cells . In vitro FGF-1 induced EMT study using NBTII rat bladder carcinoma cells
Publication Title
Modulation of several waves of gene expression during FGF-1 induced epithelial-mesenchymal transition of carcinoma cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Oryza sativa
- 20 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Lateral Organ Boundary Domain (LBD) transcription factors are specific of plants and are involved in the control of development. One LBD clade is related to the control of root development (Coudert et al., 2013, Mol. Biol. Evol. 30, 569-572). Belonging to this clade, CROWN ROOT LESS 1 controls the initiation of crown roots in rice (Inukai Plant Cell, 17, 1387-1396, Liu et al., 2005, Plant J., 43, 47-56). The aim of this study was to identify the genes that are regulated by CRL1.
Publication Title
Identification of CROWN ROOTLESS1-regulated genes in rice reveals specific and conserved elements of postembryonic root formation.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Drosophila melanogaster
- 12 Downloadable Samples
- Affymetrix Drosophila Genome Array (drosgenome1)
Description
The response of drosophila to bacterial and fungal infections involves two signaling pathways, Toll and Imd, which both activate NF-kB family members. We have studied the global transcriptional response of flies to infection with drosophila C virus. Viral infection induced a set of genes distinct from those regulated by the Toll or Imd pathways, and triggered activation of a STAT binding activity. Genetic experiments showed that the JAK kinase Hopscotch was involved in the control of the viral load in infected flies, and was required, though not sufficient, for the induction of some virus-regulated genes. Our results indicate that in addition to Toll and Imd, a third evolutionary conserved innate immunity pathway operates in drosophila and counters viral infection.
Publication Title
The Jak-STAT signaling pathway is required but not sufficient for the antiviral response of drosophila.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 20 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Human Glioblastoma Multiforme tumors taken before dendritic cell vaccination, the recurrent tumors taken after vaccination and control GBM tumors from non vaccinated patients.
Publication Title
T cells enhance stem-like properties and conditional malignancy in gliomas.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- NextSeq 500
Description
The role of sphingolipids (SLs) in the immune system has come under increasing scrutiny recently due to the emerging contributions that these important membrane components play in regulating a variety of immunological processes. The acyl chain length of SLs appears particularly critical in determining SL function. Here we show a role for very-long acyl chain SLs (VLC-SLs) in invariant natural killer T (iNKT) cell maturation in the thymus and homeostasis in the liver. Ceramide synthase 2 (CerS2) null mice, which lack VLC-SLs, were susceptible to a hepatotropic strain of lymphocytic choriomeningitis virus, which is due to a reduction in the number of iNKT cells. Bone marrow chimera experiments indicated that hematopoietic-derived VLC-SLs are essential for maturation of iNKT cells in the thymus, whereas parenchymal-derived VLC-SLs are crucial for iNKT cell survival and maintenance in the liver. Our findings suggest a critical role for VLC-SL in iNKT cell physiology. Overall design: Liver mRNA profiles of 3-4 month old wild type (WT), WT iNKT cell transfered and CerS2-/-mice, infected or not with LCMV were generated by deep sequencing. Several replicateswere included and pocessed using the MARS-seq protocol (Jaitin et al. 2014 Science.343:776-9) and sequencing in the Illumina NextSeq 500 instrument
Publication Title
Critical Role for Very-Long Chain Sphingolipids in Invariant Natural Killer T Cell Development and Homeostasis.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
15-20 cm tall 35S::Myc-GR-bdl plants were dipped headfirst in 15 µM dexamethasone or mock solution and after three hours of incubation second internodes were harvested and snap frozen in liquid nitrogen. Frozen plant material was pulverized with pestle and mortar and RNA was isolated by phenol/chlorophorm extraction as described previously (Mallory & Vaucheret 2010, PlantCell) with the modification of two additional concluding 70% EtOH washes Overall design: RNA from three samples was pooled and analyzed by RNAseq.
Publication Title
Spatial specificity of auxin responses coordinates wood formation.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
15-20 cm tall PXY:GR-MP?III/IV plants were dipped headfirst in 15 µM dexamethasone or mock solution and after three hours of incubation second internodes were harvested and snap frozen in liquid nitrogen. Frozen plant material was pulverized with pestle and mortar and RNA was isolated by phenol/chlorophorm extraction as described previously (Mallory & Vaucheret 2010, PlantCell) with the modification of two additional concluding 70% EtOH washes Overall design: RNA from three samples was pooled and analyzed by RNAseq.
Publication Title
Spatial specificity of auxin responses coordinates wood formation.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Most autoreactive B cells are normally counterselected during early B cell development. To determine whether Toll-like receptors (TLRs) regulate the removal of autoreactive B lymphocytes, we tested the reactivity of recombinant antibodies from single B cells isolated from patients deficient for IL-1R-associated kinase (IRAK)-4, myeloid differentiation factor 88 (MyD88) and UNC-93B. Indeed, all TLRs except TLR3 require IRAK-4 and MyD88 to signal and UNC-93B-deficient cells are unresponsive to TLR3, TLR7, TLR8 and TLR9. All patients suffered from defective central and peripheral B cell tolerance checkpoints resulting in the accumulation of large numbers of autoreactive mature nave B cells in their blood. Hence, TLR7, TLR8, and TLR9 may prevent the recruitment of developing autoreactive B cells in healthy donors. Paradoxically, IRAK-4-, MyD88- and UNC-93B-deficient patients did not display autoreactive antibodies in their serum nor developed autoimmune diseases, suggesting that IRAK-4, MyD88 and UNC-93B pathway blockade may thwart autoimmunity in humans.
Publication Title
IRAK-4- and MyD88-dependent pathways are essential for the removal of developing autoreactive B cells in humans.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 29 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Hepatoblastoma, the most common pediatric liver cancer, is tightly linked to excessive Wnt/�-catenin signaling. Microarray analysis identified two tumor subclasses resembling distinct phases of liver development, and a 16-gene signature discriminated invasive and metastatic hepatoblastomas, and predicted prognosis with high accuracy. <br></br>
Publication Title
Hepatic stem-like phenotype and interplay of Wnt/beta-catenin and Myc signaling in aggressive childhood liver cancer.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage, Subject
View Samples