GEO DataSets

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

12 Samples

Download data: TAB

(Submitter supplied) Dendritic cells (DCs) are rare innate immune cells that are essential regulators of anti-tumour, anti-viral and vaccine responses by the adaptive immune system. We established a protocol to differentiate human dendritic cells from iPSCs and compare their behaviour with cord blood_derived equivalents. We used bulk RNA-seq analysis to characterise the different subsets of in vitro-generated DCs including DC1, DC2A and DC2B.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

19 Samples

Download data: TXT

(Submitter supplied) Use of tape stripping for the collection of stratum corneum is a versatile and reliable procedure for the evaluation of the human skin health, including assessments of the skin barrier function, microbial content, and disease biomarkers. The tape stripping procedure is widely referenced; however, the number and type of tapes required for sample collection vary considerably, and the lack of standardized sampling, processing and normalization protocols complicate data comparison and interpretation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

24 Samples

Download data: SF

(Submitter supplied) Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically very heterogenous. To unravel phenotypically relevant MB subtypes, we compiled a harmonized proteome dataset of 167 MBs and integrated findings with DNA methylation and N-glycome data. Six proteome MB subtypes emerged, that could be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pGroup3-Myc), and synapses/immunological processes (pSHHs, pGroup3 and pGroup4). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

21 Samples

Download data: XLSX

(Submitter supplied) Understanding epithelial lineages in breast cancer and genotype-phenotype interactions requires direct measurements of the genome and transcriptome of the same single cells at scale. To achieve this, we developed wellDR-seq, the first high-genomic resolution, high-throughput method to simultaneously profile the whole genome and transcriptome of thousands of single cells. We profiled 17,427 single cells in 6 ER-positive breast cancer patients, which identified ancestral subclones in three patients that were from the luminal hormone responsive lineage, indicating a cell-of-origin. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

18 Samples

Download data: RDS

(Submitter supplied) Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically heterogenous. The application of omics technologies – mainly studying nucleic acids – has significantly improved MB classification and stratification, but treatment options are still unsatisfactory. The proteome and their N-glycans hold the potential to discover clinically relevant phenotypes and targetable pathways. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Methylation profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL13534 GPL30173 GPL23976

90 Samples

Download data: IDAT

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

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL18573 GPL30172 GPL30173

101 Samples

Download data: BED, BIGWIG, BW

(Submitter supplied) FOXA (Forkhead Box Protein A) family proteins function as pioneer transcription factors by loosening the compact chromatin structure and facilitating access for other transcription factors. The role of FOXA1 has been intensively studied in normal prostate epithelial cells and the adenocarcinoma subtype of prostate cancer (PCa) where it acts as a critical pioneer factor for the chromatin binding of androgen receptor (AR). more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30173 GPL30172

61 Samples

Download data: TXT

(Submitter supplied) FOXA (Forkhead Box Protein A) family proteins function as pioneer transcription factors by loosening the compact chromatin structure and facilitating access for other transcription factors. The role of FOXA1 has been intensively studied in normal prostate epithelial cells and the adenocarcinoma subtype of prostate cancer (PCa) where it acts as a critical pioneer factor for the chromatin binding of androgen receptor (AR). more...

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30173 GPL18573 GPL30172

24 Samples

Download data: BED, BW

(Submitter supplied) The goal of this study is to understand the transcriptomic shift during differentiatiton of iAT2s to iAT1s in 3D

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

4 Samples

Download data: H5

(Submitter supplied) Faithful genome replication is a prerequisite for cell division. In a human cell thousands of replication forks simultaneously coordinate the duplication of the entire genome. Single-molecule approaches have been invaluable to monitor this process by incorporating nucleotide analogs during replication and subsequent detection by microscopy3 or long-read sequencing. However, these methods randomly sample molecules from a large population of cells and are therefore insensitive to heterogeneity in replication dynamics between single cells. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL18573 GPL30173

50 Samples

Download data: TSV

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL30173

110 Samples

Download data

(Submitter supplied) The present prospective study included a total number of 71 patients with a final diagnosis of chronic thromboembolic pulmonary hypertension (CTEPH), who were treated by pulmonary endarterectomy (PEA) at the Kerckhoff Heart and Thorax Center between 2016 and 2020. Biopsies of the free right ventricular wall from 71 patients were collected at baseline (BL) during PEA. In a subgroup of 24 patients, myocardial interventricular septum biopsie were obtained during right heart catheterization (RHC) 12 months after PEA (postPEA) In this case, to account for technical and safety aspects, the specimens were taken from the myocardial interventricular septum. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

95 Samples

Download data: TXT

(Submitter supplied) The present prospective study included a total number of 3 patients with a final diagnosis of chronic thromboembolic pulmonary hypertension (CTEPH), who were treated by pulmonary endarterectomy (PEA) at the Kerckhoff Heart and Thorax Center between 2016 and 2020. Biopsies of the myocardial interventricular septum from 3 patients were collected at baseline (BL) before PEA surgery (pre-septal-PEA) In this case, to account for technical and safety aspects, the specimens were taken from the myocardial interventricular septum. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

6 Samples

Download data: TXT

(Submitter supplied) While del(5q) MDS patients comprise a well-defined hematological subgroup, the molecular basis underlying its origin and the reason behind the relapse to lenalidomide remains unknown. Using scRNAseq on CD34+ progenitor cells from patients with del(5q) MDS we were able to identify cells harboring the deletion, enabling us to deeply characterize the transcriptional impact of this genetic insult on disease pathogenesis and treatment response. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL30173

7 Samples

Download data: MTX, TSV, XLSX

(Submitter supplied) Long-term perturbation of de novo chromatin assembly during DNA replication has profound effects on epigenome maintenance and cell fate. The early mechanistic origin of these defects is unknown. Here, we combine acute degradation of Chromatin Assembly Factor 1 (CAF-1), a key player in de novo chromatin assembly, with single-cell genomics, quantitative proteomics, and live-microscopy to uncover these initiating mechanisms in human cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL30173

72 Samples

Download data: BED, BW, TSV

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL30173

12 Samples

Download data: BW, TXT

(Submitter supplied) Here we indentified CASZ1 as an essential regulator of the epidermal differentiation program.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

6 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

2424 Samples

Download data

(Submitter supplied) How human islet antigen reactive CD4+ memory T cells (IAR T cells) from peripheral blood affect Type 1 Diabetes (T1D) progression in the pancreas is poorly understood. We identified paired alpha/beta (TRA/TRB) T cell receptors (TCRs) in IAR T cells from the blood of healthy, at-risk, new onset, and established T1D donors, and measured sequence overlap with TCRs in pancreata from organ donors. We detected extensive TRA junction sharing between IAR T cells and pancreatic infiltrating T cells (PIT), with perfect or single mismatched TRA junction amino acid sequences comprising ~34% of unique IAR TRA junctions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

1625 Samples

Download data: CSV