Filters
Technology
Platform
Homo sapiens
15 Downloadable Samples
Illumina HiSeq 4000
Description
4 transiently expressed long non-coding RNAs that were identified in human and non-human primate cortical organoid differentiation were activated out of context in HEK293FT cells using CRISPRa. Overall design: 5 sgRNAs targeting TrEx lncRNAs or non-targeting controls were co-transfected with dCas9-VP64 into HEK293FT cells. Successfully transfected cells were selected by puromycin at 24 hours and harvested for RNA at maximal expression, 48 hours post transfection. RNA-seq libraries were prepared in biological triplicates with the NEXTflex Rapid Directional qRNA-Seq Library Prep Kit (PerkinElmer).
Publication Title
Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes.
Sample Metadata Fields
Cell line, Subject
View Samples- Caenorhabditis elegans
- 16 Downloadable Samples
- Illumina HiSeq 2000
Description
RNA-seq for monitoring expression levels in mutants that do not anchor chromatin at the nuclear periphery. Overall design: RNA-seq of depleted rRNA samples of early embryo extracts for three different genotypes: wild-type, cec-4_delta and met-2 set-25_delta_delta, in two independent biological replicas
Publication Title
Perinuclear Anchoring of H3K9-Methylated Chromatin Stabilizes Induced Cell Fate in C. elegans Embryos.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Ewing sarcoma, an osteolytic malignancy that mainly affects children and young adults, is characterized
Publication Title
DKK2 mediates osteolysis, invasiveness, and metastatic spread in Ewing sarcoma.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
The translocation t(7;12)(q36;p13) occurs in infants and very young children with AML and usually has a fatal prognosis. Whereas the transcription factor ETV6, located at chromosome 12p13, has largely been studied in different leukemia types, the influence of the translocation partner HB9 (chr. 7q36), is still unknown. This is particularly surprising as ectopic expression of HB9 is the only recurrent molecular hallmark of translocation t(7;12) AML. We investigated the influence of HB9 as a potential oncogene on cell proliferation and cell cycle in vitro, as well as on hematopoietic stem cell differentiation in vivo using murine and human model systems. We show, that HB9 induces premature senescence in human HT1080 and murine NIH3T3 cells, providing for the first time evidence for an oncogenic potential of HB9. Furthermore, HB9-transduced primary murine hematopoietic stem and progenitor cells underwent a profound differentiation arrest and accumulated at the megakaryocyte/erythrocyte progenitor stage, resulting in a premalignant myeloid cell population in vivo. Concomitantly, HB9 expression upregulates erythropoiesis-related genes in primary human hematopoietic stem and progenitor cells, and enriches gene expression profiles for cell cycle and mitosis-related biological processes. In summary, the novel findings of HB9 dependent premature senescence and perturbed hematopoietic differentiation shed light on the oncogenic properties of HB9 in translocation t(7;12) AML and offer novel targets for therapeutic intervention. Overall design: CD34+ cells were transduced with either GFP or HB9
Publication Title
The homeobox transcription factor HB9 induces senescence and blocks differentiation in hematopoietic stem and progenitor cells.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 17 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
We used microarrays to investigate gene expression changes in tumor-bearing Pax5+/- mice
Publication Title
Infection Exposure is a Causal Factor in B-cell Precursor Acute Lymphoblastic Leukemia as a Result of Pax5-Inherited Susceptibility.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 13 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
We used microarrays to investigate gene expression changes in leukemic cells from Pax5+/- mice treated with antibiotics.
Publication Title
An intact gut microbiome protects genetically predisposed mice against leukemia.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
Prostate cancer is a common cause of cancer-related death in men. E6AP, an E3 ubiquitin ligase and a transcription cofactor, is elevated in a subset of prostate cancer patients. Genetic manipulations of E6AP in prostate cancer cells expose a role of E6AP in promoting growth and survival of prostate cancer cells in vitro and in vivo. However, the effect of E6AP on prostate cancer cells is broad and it cannot be explained fully by previously identified tumour suppressor targets of E6AP, promyelocytic leukemia protein and p27. To explore additional players that are regulated downstream of E6AP, we combined a transcriptomic and proteomic approaches. We identified and quantified 16,130 transcripts and 7,209 proteins in castration resistant prostate cancer cell line, DU145. A total of 2,763 transcripts and 308 proteins were significantly altered upon knockdown of E6AP. Pathway analyses supported the known phenotypic effects of E6AP knockdown in prostate cancer cells and in parallel exposed novel potential links of E6AP with cancer metabolism, DNA damage repair and immune response. Changes in expression of the top candidates were confirmed using real-time polymerase chain reaction. Of these, clusterin, a stress-induced chaperone protein, commonly deregulated in prostate cancer, was pursued further. Knockdown of E6AP resulted in increased clusterin transcript and protein levels in vitro and in vivo. Concomitant knockdown of E6AP and clusterin supported the contribution of clusterin to the phenotype induced by E6AP. Overall, results from this study provide insight into the potential biological pathways controlled by E6AP in prostate cancer cells and identifies clusterin as a novel target of E6AP. Overall design: Examination of candidate targets regulated by E6AP at transcript level
Publication Title
Proteotranscriptomic Measurements of E6-Associated Protein (E6AP) Targets in DU145 Prostate Cancer Cells.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 42 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Lmo2 expression defines tumor cell identity during T-cell leukemogenesis.
Sample Metadata Fields
Age, Specimen part, Disease, Disease stage
View Samples
GSE59325- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Analysis of perirenal adipose tissue from healthy kidney donors (age 449 years, BMI 25.83.3 kg/m2, meanSD).
Publication Title
FTO Obesity Variant Circuitry and Adipocyte Browning in Humans.
Sample Metadata Fields
Specimen part
View Samples- Glycine max
- 27 Downloadable Samples
- Affymetrix Soybean Genome Array (soybean)
Description
The autoregulation of mycorrhization (AOM) describes a plant regulatory mechanism that limits the number of infection events by arbuscular mycorrhizal fungi. The key signal mediator is a receptor kinase (GmNARK) that acts in the shoots. Early signals of the mycorrhizal symbiosis induce a root-derived signal that activates GmNARK in the shoot finally leading to a systemic repression of subsequent infections in the root. So far, less is known about the signals down-stream of GmNARK. To find genes regulated by GmNARK in a mycorrhiza-dependent as well as in a mycorrhiza-independent manner, we used the Affymetrix GeneChip for soybean. In general, mycorrhizal root systems consist of both colonized and non-colonized, but autoregulated roots. To physically separate those two root types for transcript analysis of specifically regulated genes, we used the split-root system. Transcript profiling during AOM was done with material of Bragg wild-type and of the nark mutant nts1007, either non-inoculated or partially inoculated with the mycorrhizal fungus Rhizophagus irregularis (formerly Glomus intraradices). Wild-type and nark mutants were inoculated with R. irregularis on one half of the root-systems (root-parts "A") only. The remaining half of the root-systems stayed non-infected (root-parts "B"). Corresponding controls stayed completely non-infected. Gene expression was analyzed in inoculated root-parts, non-inoculated root-parts and shoots of three individual plants per treatment. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Sara Schaarschmidt. The equivalent experiment is GM53 at PLEXdb.]
Publication Title
Analyzing the soybean transcriptome during autoregulation of mycorrhization identifies the transcription factors GmNF-YA1a/b as positive regulators of arbuscular mycorrhization.
Sample Metadata Fields
Age, Specimen part
View Samples