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Items: 1 to 20 of 383

1.

Pluripotent stem cells related to embryonic disc exhibit common self-renewal requirements in diverse livestock species

(Submitter supplied) Despite four decades of effort, robust propagation of pluripotent stem cells from livestock animals remains challenging. The requirements for self-renewal are unclear and the relationship of cultured stem cells to pluripotent cells resident in the embryo uncertain. Here we avoided feeder cells or serum factors to provide a defined culture microenvironment. We show that the combination of Activin A, Fibroblast growth factor, and Wnt inhibitor XAV939 (AFX), supports establishment and continuous expansion of pluripotent stem cell lines from porcine, ovine and bovine embryos. more...
Organism:
Bos taurus; Sus scrofa; Ovis aries
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL26351 GPL26012 GPL27721
33 Samples
Download data: TXT
Series
Accession:
GSE172420
ID:
200172420
2.

Diverse human astrocyte and microglial transcriptional responses to Alzheimer’s pathology

(Submitter supplied) To better define roles that microglia and astrocytes play in Alzheimer’s disease (AD), we used single-nuclei RNA-sequencing to comprehensively characterize transcriptomes in these glial nuclei isolated post mortem from non-diseased control and neuropathologically-defined AD brains. Genes associated with AD risk were highly represented, especially in microglia. Transcriptome differences significantly correlated with immunohistochemical phospho-Tau (pTau) density included genetic risk genes for both microglia (APOE, BIN1, MS4A6A, PILRA) and astrocytes (APOE, CLU, MEF2C, IQCK). more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20301
24 Samples
Download data: TAR
Series
Accession:
GSE160936
ID:
200160936
3.

­De novo DNA methylation suppresses aberrant fate trajectory during epiblast transition [ATAC-seq]

(Submitter supplied) Genome remethylation is essential for mammalian development. Here we examined cell fate in the absence of de novo DNA methyltransferases. We found that embryonic stem (ES) cells deficient for Dnmt3a and Dnmt3b are rapidly eliminated from chimaeras. Pluripotency progression is derailed towards extra-embryonic trophoblast. This aberrant trajectory is propelled by failure to methylate and suppress expression of Ascl2 during formative transition. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
14 Samples
Download data: BW
Series
Accession:
GSE158344
ID:
200158344
4.

De novo DNA methylation suppresses aberrant fate trajectory during epiblast transition [RNA-seq]

(Submitter supplied) Genome remethylation is essential for mammalian development. Here we examined cell fate in the absence of de novo DNA methyltransferases. We found that embryonic stem (ES) cells deficient for Dnmt3a and Dnmt3b are rapidly eliminated from chimaeras. Pluripotency progression is derailed towards extra-embryonic trophoblast. This aberrant trajectory is propelled by failure to methylate and suppress expression of Ascl2 during formative transition. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
4 Samples
Download data: TSV
Series
Accession:
GSE158310
ID:
200158310
5.

Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory

(Submitter supplied) Genome remethylation is essential for mammalian development but specific reasons are unclear. Here we examined embryonic stem (ES) cell fate in the absence of de novo DNA methyltransferases. We observed that ES cells deficient for both Dnmt3a and Dnmt3b are rapidly eliminated from chimeras. On further investigation we found that in vivo and in vitro the formative pluripotency transition is derailed toward production of trophoblast. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
18 Samples
Download data: BW
Series
Accession:
GSE158347
ID:
200158347
6.

Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in lewy body diseases

(Submitter supplied) Parkinson’s disease (PD), Parkinson’s disease with dementia (PDD) and dementia with Lewy bodies (DLB) are three clinically, genetically and neuropathologically overlapping neurodegenerative diseases collectively known as the Lewy body diseases (LBDs). A variety of molecular mechanisms have been implicated in PD pathogenesis, but the mechanisms underlying PDD and DLB remain largely unknown, a knowledge gap that presents an impediment to the discovery of diseasemodifying therapies. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20301
28 Samples
Download data: TAR
Series
Accession:
GSE178146
ID:
200178146
7.

Striatal transcriptome changes linked to drug-induced repetitive behaviors

(Submitter supplied) Disruptive or excessive repetitive motor patterns (stereotypies) are cardinal symptoms in numerous neuropsychiatric disorders. Stereotypies are also evoked by psychomotor stimulants such as amphetamine. The acquisition of motor sequences are paralleled by changes in activity patterns in the striatum, and stereotypies have been linked to abnormal plasticity in these reinforcement-related circuits. Here, we designed experiments in mice to identify transcriptomic changes that underlie striatal plasticity occurring alongside the development of drug-induced stereotypic behavior. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
18 Samples
Download data: TXT
Series
Accession:
GSE157913
ID:
200157913
8.

Whole genome expression profiling based on paraffin embedded tissue of a large DLBCL cohort

(Submitter supplied) Gene expression profiling was carried out for RNA extracted from Formalin-fixed, paraffin embedded (FFPE) biopsies for 1311 patients with diffuse large b-cell lymphoma (DLBCL) using the Illumina DASL platform.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL14951
1310 Samples
Download data: TXT
Series
Accession:
GSE181063
ID:
200181063
9.

IL-4-BATF signaling directly modulates IL-9 producing mucosal mast cell (MMC9) function in experimental food allergy

(Submitter supplied) IL-4-BATF signaling directly modulates IL-9 producing mucosal mast cell (MMC9) function in experimental food allergy
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
84 Samples
Download data: TXT
Series
Accession:
GSE179304
ID:
200179304
10.

Neonatal Blood Spots from the Emory University African American Microbiome in Pregnancy Cohort

(Submitter supplied) Newborn screening blood spots were obtained for neonates born to women enrolled in the Emory University African American Microbiome in Pregnacy Cohort
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL23976
42 Samples
Download data: IDAT
Series
Accession:
GSE154446
ID:
200154446
11.

Fibroblast Growth Factor Receptor 3 Alterations and Response to Immune Checkpoint Inhibition in Metastatic Urothelial Cancer: A Real World Experience

(Submitter supplied) Purpose: We evaluated clinical outcomes of patients with FGFR3-altered metastatic UC treated with ICB and investigate the underlying immunogenomic mechanisms of response and resistance Methods: 103 patients with metastatic UC treated with ICB at a single academic medical center from 2014-2018 were identified. Clinical annotation for demographics and cancer outcomes, as well as somatic DNA and RNA sequencing were performed. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24014
90 Samples
Download data: CSV, TXT
Series
Accession:
GSE176307
ID:
200176307
12.

Human blastocyst model by self-organization of naïve pluripotent stem cells

(Submitter supplied) Human naïve pluripotent cells can differentiate to extraembryonic trophoblast and hypoblast cells. Here we report formation of human blastocyst models by self-organization solely of naïve pluripotent stem cells. The embryo models comprise the three founding lineages, epiblast, trophoblast and hypoblast, arranged to mimic the natural blastocyst. Single-cell RNA sequencing validated the identity of each cell type.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
495 Samples
Download data: CSV, TXT
Series
Accession:
GSE171820
ID:
200171820
13.

Transcriptomic profile of normal immortalized fallopian tube cells in response to long-term norepinephrine treatment

(Submitter supplied) The goal of this study was to identify transcriptional changes that occur in response to long-term norepinephrine (NE) treatment on normal immortalized fallopian tube cells (iFTSEC283). We treated isogenic cell lines (iFTSEC283 and iFTSEC283p53R175H) with 10μM NE or vehicle control (water) for 137 days with media change every two days followed by whole-transcriptome RNA seq. We identified 123 differentially expressed genes in 10μM NE vs mock-treated iFTSEC283. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
12 Samples
Download data: XLSX
Series
Accession:
GSE168097
ID:
200168097
14.

Triple negative, JAK2V617F and CALR mutated essential thrombocythaemia patients share a unique gene expression signature

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Methylation profiling by genome tiling array
Platforms:
GPL16791 GPL23976
56 Samples
Download data: IDAT, TXT
Series
Accession:
GSE156547
ID:
200156547
15.

Triple negative, JAK2V617F and CALR mutated essential thrombocythaemia patients share a unique gene expression signature [array]

(Submitter supplied) Using gene expression analysis in combination with genome-wide methylation profiling, we discovered a unique signature pattern that is consistent across the essential thrombocythaemia population regardless of mutation status.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL23976
34 Samples
Download data: IDAT, TXT
Series
Accession:
GSE156546
ID:
200156546
16.

Triple negative, JAK2V617F and CALR mutated essential thrombocythaemia patients share a unique gene expression signature [RNA-seq]

(Submitter supplied) There is a unique signature pattern that is consistent across the essential thrombocythaemia (ET) population regardless of mutation status. ET phenotype may therefore, at least in part and regardless of mutation type, be driven by transcriptional mis-regulation and may propagate downstream via the MAPK, TNF and NFκB pathways with resultant JAK/STAT activation.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
22 Samples
Download data: TXT
Series
Accession:
GSE156336
ID:
200156336
17.

Human Naïve Epiblast Cells Possess Unrestricted Lineage Potential II

(Submitter supplied) Transcriptomic analysis confirms the trophoblast identity of the naïve pluripotent stem cell derived TSC cultures by comparing to the placenta derived TSC culture.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
14 Samples
Download data: TXT
Series
Accession:
GSE167089
ID:
200167089
18.

Human Naïve Epiblast Cells Possess Unrestricted Lineage Potential

(Submitter supplied) Classical mouse embryology has established a paradigm of early development drivenby sequential lineage bifurcations. Accordingly, mouse embryonic stem cells derivedfrom early epiblast have lost the potency to produce extraembryonic trophectoderm.We show in contrast that human naive epiblast cells readily make trophectoderm.Inhibition of ERK signalling, instrumental in naive stem cell propagation, unexpectedlypotentiates trophectoderm formation, an effect enhanced by Nodal inhibition.Transcriptome analyses authenticate conversion into trophectoderm with subsequentproduction of syncitiotrophoblast, cytotrophoblast and trophoblast stem cells. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
20 Samples
Download data: TXT
Series
Accession:
GSE166422
ID:
200166422
19.

Human Naïve Epiblast Cells Possess Unrestricted Lineage Potential

(Submitter supplied) Classical mouse embryology has established a paradigm of early development drivenby sequential lineage bifurcations. Accordingly, mouse embryonic stem cells derivedfrom early epiblast have lost the potency to produce extraembryonic trophectoderm.We show in contrast that human naive epiblast cells readily make trophectoderm.Inhibition of ERK signalling, instrumental in naive stem cell propagation, unexpectedlypotentiates trophectoderm formation, an effect enhanced by Nodal inhibition.Transcriptome analyses authenticate conversion into trophectoderm with subsequentproduction of syncitiotrophoblast, cytotrophoblast and trophoblast stem cells. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
64 Samples
Download data: TXT
Series
Accession:
GSE166401
ID:
200166401
20.

Asah2 represses the p53-Hmox1 axis to protect myeloid-derived suppressive cells from ferroptosis

(Submitter supplied) Myeloid-derived suppressor cells (MDSCs) are immune suppressive cells that massively accumulate under pathological conditions to suppress T cell immune response. Dysregulated cell death contributes to MDSC accumulation, but the molecular mechanism underlying this cell death dysregulation is not fully understood. We report here that neutral ceramidase (N-acylsphingosine amidohydrolase, ASAH2) is highly expressed in tumor-infiltrating MDSCs in colon carcinoma and acts as a MDSC survival factor. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL16570
4 Samples
Download data: CEL, XLSX
Series
Accession:
GSE163399
ID:
200163399
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