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GSE15248
Homo sapiens
6 Downloadable Samples
Illumina human-6 v2.0 expression beadchip
Description
A Transcriptomics Approach to Study the Biocompatibility and Finding out the Potential Applications of Magnetite (Fe3O4) Nanoparticles
Publication Title
Magnetite (Fe3O4) nanocrystals affect the expression of genes involved in the TGF-beta signalling pathway.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 11 Downloadable Samples
Illumina HiSeq 2500
Description
To explore potential molecular mechanisms underlying the temporal process of DNA damage and repair in CSCs, we utilized deep RNA sequencing to analyze the expression of DNA damage and repair-associated genes at the transcriptome level. Our gene set analysis of CSCs and matched non-CSCs revealed a stemness-associated upward trend of global gene expression, particularly in NHEJ, mismatch excision repair (MMR) and HR pathways. Overall design: The RNA profiles of IN528, T3961, and T4121 CSCs and matched non-CSCs were generated by deep sequencing.
Publication Title
Temporal DNA-PK activation drives genomic instability and therapy resistance in glioma stem cells.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 3 Downloadable Samples
- NextSeq 500
Description
We here addressed the question whether the unique capacity of mesenchymal stromal/stem cells (MSCs) to re-establish tissue homeostasis depends on their potential to sense pathogen associated molecular pattern (PAMP) and, in consequence, mount an adaptive response in the interest of tissue repair. After injection of MSCs which had been primed with the bacterial wall component LPS into murine wounds, an unexpected acceleration of healing occurred, clearly exceeding that of non-primed MSCs. This correlates with a fundamental reprogramming of the transcriptome in LPS treated MSCs as deduced from RNA-seq analysis and its validation. A network of genes mediating the adaptive response through the TLR-4 pathway responsible for neutrophil activation (GCP- 2, ENA-78, IL-1ß IL-8) and MSC protection (SOX6) profoundly contributes to enhanced wound healing. In fact, silencing of either TRL-4, or IRAK3, a downstream effector of TRL-4, or SOX6 suppressed wound healing most likely due to suppression of neutrophil extracellular trap formation and suppression of the enhanced microbicidal release of reactive oxygen species (ROS), key features of neutrophil activation. This previously unreported results uncover SOX6 which protects MSCs at the wound site from enhanced oxidative stress. This unprecedented findings hold substantial promise to refine current MSC-based therapies for difficult-to-treat wounds. Overall design: Transcriptome profiling of MSCs
Publication Title
TLR4-dependent shaping of the wound site by MSCs accelerates wound healing.
Sample Metadata Fields
Treatment, Subject
View Samples- Danio rerio
- 4 Downloadable Samples
- IlluminaGenomeAnalyzerIIx
Description
We have sequenced the polysome-associated translating mRNAs from stage-matched wild-type and eif3ha morphant embryos at ~24 hpf stage to identify transcripts translationally regulated by eIF3ha. As a control, we have also sequenced total mRNAs from the stage-matched wild-type and eif3ha morphants as well at ~ 24 hpf. Overall design: Polysome-associated mRNAs were isolated from 300 zebrafish embryos. Total RNA was isolated from 50 zebrafish embryos. Single 36-base pair reads were sequenced on the Illumina Genome Analyzer Iix.
Publication Title
Translation initiation factor eIF3h targets specific transcripts to polysomes during embryogenesis.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 570 Downloadable Samples
- NextSeq 500
Description
We report the comparative gene expression between embryonic stem cell derived cranial and spinal motor neurons and multiple time points after induction and primary cultured ocular and spinal motor neurons, using single cell RNA sequencing. Overall design: Single neurons were isolated in 96-well plates and their gene expression profiled using SMART-Seq2 from 8 samples: (1-2) primary cultured oculomotor/trochlear motor neurons and spinal motor neurons collected at embryonic day E11.5 and cultured for 7 days, (3-8) ESC-derived induced cranial and spinal motor neurons at either 2 days, 5 days, or 7 days after plating.
Publication Title
Stem cell-derived cranial and spinal motor neurons reveal proteostatic differences between ALS resistant and sensitive motor neurons.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 22 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Modeling a lethal prostate cancer variant with small-cell carcinoma features.
Sample Metadata Fields
Specimen part, Disease
View Samples- Homo sapiens
- 22 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Purpose: Small-cell prostate carcinoma (SCPC) morphology predicts for a distinct clinical behavior, resistance to androgen ablation, and frequent but short responses to chemotherapy. The model systems we report reflect the biology of the human disease and can be used to improve our understanding of SCPC and to develop new therapeutic strategies for it.
Publication Title
Modeling a lethal prostate cancer variant with small-cell carcinoma features.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 18 Downloadable Samples
- Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
In vivo profiling of hypoxic gene expression in gliomas using the hypoxia marker EF5 and laser-capture microdissection
Publication Title
In vivo profiling of hypoxic gene expression in gliomas using the hypoxia marker EF5 and laser-capture microdissection.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 18 Downloadable Samples
- Illumina HiSeq 2000
Description
Plant Homeo Domain (PHD) is a versatile chromatin reader/effector module which recognizes methylated, acetylated or unmodified histone substrates and regulates cellular gene expression programs. Although PHD domains shows selective epigenetic recognition of methylated, acetylated and unmodified histone substrates, there has been no previous report on its catalytic function regulating malignant transformation of cells. Here we report that PHD finger of UBR7 (Ubiquitin Protein Ligase E3 Component N-Recognin 7 (Putative)), in isolation or in context of full length protein, harbors E3 ubiquitin ligase activity towards monoubiquitination of histone H2B at lysine 120 . Knockdown of UBR7 in MCF10a and breast cancer cells decreased H2BK120ub both at the global levels and on specific genes. Conversely, overexpression of wild type, but not catalytic mutant, rescued H2BK120ub levels. Low UBR7 expression was associated with basal-like and triple negative breast cancers as well as showed poor expression in metastatic tumors. Consistently, UBR7 loss resulted in invasion properties, induced epithelial-to-mesenchymal transition and promoted metastasis. Conversely, ectopic expression of UBR7 reduced cell growth, invasion and tumor growth in mouse fat pad. Mechanistically, UBR7 reduced H2BK120ub gene body of cell-adhesion related genes as well as gene expression including on CDH4 gene. Importantly, rebuilding CDH4 levels rescued invasion phenotypes seen in UBR7-low cells. Collectively, our results establish that UBR7 PHD has novel H2B ubiquitin ligase activity and it suppresses tumor growth in basal-like breast cancers. Overall design: Triplicate total RNA profiles in Wild Type and UBR7-shRNA MCF10A Cell Line
Publication Title
Atypical plant homeodomain of UBR7 functions as an H2BK120Ub ligase and breast tumor suppressor.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
We assessed the gene expression profile of purified CD205+CD8+ Dendritic Cells isolated from murine spleens.
Publication Title
NOD2 modulates immune tolerance via the GM-CSF-dependent generation of CD103<sup>+</sup> dendritic cells.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples