GEO DataSets

(Submitter supplied) Advanced stem cell-based in vitro models of embryogenesis offer great promise to decipher developmental programs with high-throughput and resolution. However, the rapid changes in morphology and cell state that underly these models mask multiple higher order parameters, including the regulative balance between differentiation and self-renewal that govern transient progenitor cell populations. Here, we apply a continuous single-cell Cas9-based molecular recorder to mouse embryonic stem cells, which enables the recovery of can reproducibly recovere and high-content information regarding the historical relationship between individual cells. more...

Organism:

Mus musculus; synthetic construct

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL17769 GPL24247 GPL26526

29 Samples

Download data: TAR, TSV, TXT

(Submitter supplied) Non-coding regions of the genome contain cis-regulatory elements (CREs) that govern transcriptional activity critical for development and physiologic functions of major metabolic tissues, such as islets, adipose, liver, and skeletal muscle. Moreover, they contain the majority of genetic variants associated with risk of type 2 diabetes and quantitative alterations in related metabolic phenotypes. Here, we defined comprehensive, representative CRE maps of these major metabolic tissues in mice of both sexes using ATAC-seq and incorporating genetic variation of the 8 major Collaborative Cross founders and diet-response. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

386 Samples

Download data: BED, BIGWIG, NARROWPEAK

(Submitter supplied) Extensive genome analysis of pregnancy loss products by genome haplarithmisis. Pregnancy loss (PL) is the primary pregnancy complication, mostly caused by chromosomal abnormalities of the conceptus. However, the nature and prevalence of these abnormalities and the allocation of (ab)normal cells in embryonic and placental compartments during intrauterine development remains elusive. We analyzed 1,745 spontaneous PLs and found that ~50% were karyotypically normal. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL28939

450 Samples

Download data: IDAT, TXT

(Submitter supplied) Extensive genome analysis of pregnancy loss products by genome haplarithmisis. Pregnancy loss (PL) is the primary pregnancy complication, mostly caused by chromosomal abnormalities of the conceptus. However, the nature and prevalence of these abnormalities and the allocation of (ab)normal cells in embryonic and placental compartments during intrauterine development remains elusive. We analyzed 1,745 spontaneous PLs and found that ~50% were karyotypically normal. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

13 Samples

Download data: IDAT

(Submitter supplied) Accurate pathological diagnosis is crucial for optimal management of cancer patients. For a number of hematolymphoid tumor entities, standardization of the diagnostic process has been shown to be particularly challenging - with substantial inter-observer variability in the histopathological diagnosis of many tumor types. Genome-wide DNA methylation profiling has been shown to contribute to accurate and precise tumor classification and diagnosis in several tumor types, including central nervous system neoplasms. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Third-party reanalysis

Platforms:

GPL23976 GPL13534

989 Samples

Download data: CSV, IDAT, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26208 GPL17639

21 Samples

Download data

(Submitter supplied) We performed RNA-Seq based gene expression analysis of Arabidopsis Col-0 plants grown in presence of SynComCol-0 (eubiotic bacterial community), SynCommfec (dysbiotic bacterial community) and Axenic conditions in GnotoPot plant gnotobiotic growth system. SynCom preparation was done by mixing equal ratio of the each strain measured based on optical density of (OD600) in 10 mM MgCl2 and adjusting to the final combined OD600 of 0.04. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

9 Samples

Download data: CSV

(Submitter supplied) Even amongst genetically identical cancer cells, therapy resistance often only emerges from a very small subset of those cells. Much effort has gone into uncovering the molecular differences in rare individual cells in the initial population that may allow certain cells to become therapy resistant; however, comparatively little is known about variability in the resistant outcomes themselves. Here, we develop and apply FateMap, a framework that combines DNA barcoding with single-cell RNA sequencing to reveal the fates of hundreds of thousands of clones exposed to anti-cancer therapies. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

115 Samples

Download data: TSV

(Submitter supplied) We profiled the transcritpome and ATAC profiles of human pancreatic islets generated from pluripotent stem cells. Multiomic profiling was also performed on primary human islets and in vivo matured SC-islets for comparision. We catalogued the ATAC associated signatures for each cell types in SC-islets and compared them to their human primiary islet counterparts. In vivo maturation of SC-islets were also compared with in vitro SC-islets. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

36 Samples

Download data: BED, CSV, H5, TBI, TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL18573

41 Samples

Download data

(Submitter supplied) Pancreatic islet cells derived from human pluripotent stem cells hold great promise for modeling and treating diabetes. Differences between stem cell-derived and primary islets remain, but molecular insights to inform improvements are limited. Here, we acquire single-cell transcriptomes and accessible chromatin profiles during in vitro islet differentiation and from primary childhood and adult pancreas for comparison. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

3 Samples

Download data: H5AD

(Submitter supplied) Pancreatic islet cells derived from human pluripotent stem cells hold great promise for modeling and treating diabetes. Differences between stem cell-derived and primary islets remain, but molecular insights to inform improvements are limited. Here, we acquire single-cell transcriptomes and accessible chromatin profiles during in vitro islet differentiation and from primary childhood and adult pancreas for comparison. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

5 Samples

Download data: H5AD, MTX, TXT

(Submitter supplied) Pancreatic islet cells derived from human pluripotent stem cells hold great promise for modeling and treating diabetes. Differences between stem cell-derived and primary islets remain, but molecular insights to inform improvements are limited. Here, we acquire single-cell transcriptomes and accessible chromatin profiles during in vitro islet differentiation and from primary childhood and adult pancreas for comparison. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

5 Samples

Download data: H5AD, MTX, TXT

(Submitter supplied) Pancreatic islet cells derived from human pluripotent stem cells hold great promise for modeling and treating diabetes. Differences between stem cell-derived and primary islets remain, but molecular insights to inform improvements are limited. Here, we acquire single-cell transcriptomes and accessible chromatin profiles during in vitro islet differentiation and from primary childhood and adult pancreas for comparison. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: H5AD

(Submitter supplied) Pancreatic islet cells derived from human pluripotent stem cells hold great promise for modeling and treating diabetes. Differences between stem cell-derived and primary islets remain, but molecular insights to inform improvements are limited. Here, we acquire single-cell transcriptomes and accessible chromatin profiles during in vitro islet differentiation and from primary childhood and adult pancreas for comparison. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: BED, NARROWPEAK, XLS

(Submitter supplied) Epigenetic immunomodulation by association of guadecitabine with ipilimumab (NIBIT-M4 Phase Ib trial, NCT02608437) has been shown to be safe and tolerable in advanced melanoma and to have significant immunomodulatory and antitumor activity [Di Giacomo et al. Clin Cancer Res. 2019 Dec 15;25(24):7351-7362]. Here we carried out a multi-omics assessment of pre-therapy (week 0, w0) and on-treatment (week 4, w4 and week 12, w12) tumor biopsies from enrolled patients looking at the specific parameters that could explain clinical benefit vs treatment failure. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL32584

40 Samples

Download data: RCC

(Submitter supplied) Glioblastoma multiforme (GBM) is the most common and aggressive primary malignant brain tumor, but the current therapeutic approaches have very limited impact on increase of the patients’s survival with GBM. Our recent clinical trial with autologous activated nature killer (NK) cells (AKCs) including 14 patients with recurrent GBM found that the progression-free and overall survival times were significantly increased in some patients in the treatment group. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL32232

12 Samples

Download data: RCC

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL21145

513 Samples

Download data: IDAT

(Submitter supplied) The histopathological diagnosis of sinonasal tumors is challenging as it encompasses a heterogeneous spectrum of various differential diagnoses as well as poorly defined, disputed entities such as sinonasal undifferentiated carcinomas (SNUCs). In this study, we show that a machine learning algorithm based on DNA methylation is able to classify sinonasal tumors with clinical-grade reliability. We further show that tumors with SNUC morphology are not as undifferentiated as their current terminology suggests, but can be assigned to four molecular classes defined by distinct epigenic, mutational and proteomic profiles. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL21145 GPL13534

461 Samples

Download data: CSV, IDAT

(Submitter supplied) Here we describe a single-cell atlas of aging for virtually every cell type of the nematode Caenorhabditis elegans. Our findings suggest that C. elegans aging is not random in nature, but rather characterized by coordinated changes in functionally related metabolic and stress-response genes in a highly cell-type specific fashion. Aging signatures of different cell types are largely different from one another, with downregulation of energy metabolism being the only nearly universal change. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22765

11 Samples

Download data: MTX, TSV