GEO DataSets

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

Organism:

Homo sapiens; Drosophila melanogaster; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL25537 GPL19415

143 Samples

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(Submitter supplied) Gene expression is regulated by controlling distinct steps of the transcriptional cycle, including initiation, pausing, elongation, and termination. Kinases phosphorylate RNA Polymerase II and associated factors to control transitions between these steps and act as central gene regulatory nodes. Similarly, phosphatases that dephosphorylate these components are emerging as important regulators of transcription, though their roles remain less well understood. more...

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19415

94 Samples

Download data: BW

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

Organism:

Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL19415 GPL18573 GPL19057

43 Samples

Download data: RESULTS

(Submitter supplied) HNF1B (Hepatocyte Nuclear Factor 1-Beta) is a POU-homeobox transcription factor expressed in kidney and frequently mutated in patients suffering from Congenital Anomalies of the Kidney and the Urinary Tract (CAKUT). HNF1B is a bookmarking factor, able to bind mitotic chromatin and necessary for the post-mitotic reactivation of gene expression. In order to characterize the molecular functions of HNF1B as a bookmarking factor, we performed ChIPseq on asynchronous and mitotic renal cells. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19415

14 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) The Polycomb system plays fundamental roles in regulating gene expression during mammalian development. However, how it controls transcription to enable gene repression has remained enigmatic. Here we employ rapid degron-based depletion coupled with live-cell transcription imaging and single-particle tracking to uncover how the Polycomb system controls transcription in single cells. We discover that the Polycomb system is not a constitutive block to transcription but instead sustains a long-lived deep promoter OFF-state which limits the frequency with which the promoter can enter into a transcribing state. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19415

12 Samples

Download data: BW

(Submitter supplied) Purpose: 1. Compare transcriptomes of hESC-derived MSCs (EMSCs) and somatic MSCs (SMCS); 2. Reveal transriptomic profiles of EMSCs post injection into mouse blastocyst. Methods: For bulk seq on cultured human MSCs, mRNA was isolated using RNeasy Mini Kit (QIAGEN) and libraries was constructed using an Illumina kit, and then sequenced on NovaSeq platform. For single cell (sc) RNAseq on cultured human MSCs, cells were dissociated and lysed in the Oil-droplet Single Cell Capture System (Nadia Dolomite) and libraries were constructed using Nextera kits (Illumina), and then sequenced on Hiseq 150PE (Illumina). more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL19415

14 Samples

Download data: CSV, TXT

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

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19415 GPL18573

24 Samples

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(Submitter supplied) Prostate cancer is a unique disease from a metabolic perspective. Early stage localized prostate cancer does not typically display increased aerobic glycolysis (the Warburg effect), as seen in other malignancies. However, increasing evidence suggests that advanced prostate cancer exhibits the Warburg effect and displays high glucose uptake. We describe here that trans-gnetin H (TGH), a naturally-occurring resveratrol trimer extracted from Paeonia suffruticosa, displays significant anti-cancer effects in advanced prostate cancer cells xenografted PC-3 cells in vivo.TGH perturbs energy metabolism by blocking the availability of glucose and inducing profound metabolic and transcriptomic changes in prostate cancer cells as demonstrated by RNA-seq. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19415

18 Samples

Download data: TXT

(Submitter supplied) Droplet microfluidic methods have massively increased the throughput of single-cell RNA sequencing campaigns. The benefit of scale-up is, however, accompanied by increased background noise when processing challenging samples as well as lower overall RNA capture efficiency. These drawbacks stem from the lack of strategies to enrich for high-quality material at the moment of cell encapsulation and the lack of implementable multi-step enzymatic processes that increase RNA capture. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL18573 GPL19415

16 Samples

Download data: CSV, TXT

(Submitter supplied) Nintedanib is a potent anti-fibrotic angio-kinase inhibitor, which has shown clinical efficacy in combination with chemotherapy in locally advanced muscle invasive BC patients. Nintedanib inhibits Fibroblast Growth Factor receptors (FGFRs), validated targets in patients with BC harboring FGFR3/2 genetic alterations. Here, we aimed at studying its mechanisms of action to understand therapy their combination (n=4). more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19415

16 Samples

Download data: TXT

(Submitter supplied) Nintedanib is a potent anti-fibrotic angio-kinase inhibitor, which has shown clinical efficacy in combination with chemotherapy in locally advanced muscle invasive BC patients. Nintedanib inhibits Fibroblast Growth Factor receptors (FGFRs), validated targets in patients with BC harboring FGFR3/2 genetic alterations. Here, we aimed at studying its mechanisms of action to understand therapy their combination (n=4). more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19415

17 Samples

Download data: TXT

(Submitter supplied) When combined into spheres and embedded in extracellular matrix, hetero-cellular cultures of pancreatic cancer and stellate cells produce invasive, stellate-led, projections. In order to establish what cancer and stellate cells are expressing in this context we generated chimeric spheres of mouse and human cells. Invasive spheroids could then be processed for RNA sequencing, with reads mapped back to parent species and thus cell type.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19415

10 Samples

Download data: XLSX

(Submitter supplied) We present DEFND-seq (DNA and Expression From Nucleosome Depletion), a scalable method for co-sequencing RNA and DNA from single nuclei. In DEFND-seq we treat nuclei with lithium diiodosalicylate to disrupt chromatin and expose genoimc DNA. The nuclei are then tagmented with Tn5 transposase, which fragments and tags gDNA. Tagmented nuclei are loaded into a microfluidic droplet generator which combines nuclei, beads containing transcriptomic and genomic barcodes, and reverse transcription reagents into single droplets. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

5 related Platforms

13 Samples

Download data: TSV, TXT

(Submitter supplied) Transcription must be highly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, we reveal that actively transcribed CpG island-associated gene promoters recruit SET1 chromatin modifying complexes to enable gene expression. more...

Organism:

Homo sapiens; Drosophila melanogaster; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL25537 GPL19057 GPL19415

60 Samples

Download data: BED, BW, CSV

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

Organism:

Homo sapiens; Mus musculus; Drosophila melanogaster

Type:

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

Platforms:

GPL19057 GPL19415 GPL25537

124 Samples

Download data

(Submitter supplied) PSEN1 ΔE9 mutation causes a familial form of Alzheimer's disease. We have previously shown that human induced pluripotent stem cell (iPSC)-derived astrocytes carrying PSEN1 ΔE9 mutation exhibit transcriptional and functional abnormalities (Stem Cell Reports. 2017;9:1885-1897). Here we injected glial progenitors derived from 2 pairs of PSEN1 ΔE9 mutant- isogenic CTRL iPSCs intracerebroventricularly into newborn mice. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19415

11 Samples

Download data: TXT

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

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL19057 GPL18573 GPL19415

87 Samples

Download data: TSV

(Submitter supplied) We developed the first droplet-based single-cell total-RNA-seq method. We refer to this platform as Multiple Annealing and Tailing-based Quantitative scRNA-seq in Droplet (MATQ-Drop). With the detection of nascent RNA species, we showed that the cell atlas of human brain samples could be effectively constructed based on nascent RNA species. Furthermore, we observed that only lncRNA species are sufficient to construct the cell atlas, suggesting that MATQ-Drop allows a large-scale identification of the cell-type-specific lncRNA species. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL19415 GPL18573

47 Samples

Download data: TSV

(Submitter supplied) The breast tumour microenvironment (TME) includes fibroblasts, adipocytes, inflammatory and immune cells. While treatment of tumours with chemotherapeutic agents such as Docetaxel, leads to apoptosis of tumour cells, it can also have consequences for the cellular makeup and transcriptional profile of the TME and these, like increased epithelial mesenchymal transition can promote undesirable consequences, such as Cancer Stem Cell development. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19415

13 Samples

Download data: CSV

(Submitter supplied) Transcriptional heterogeneity among malignant cells of a tumor has been studied in individual cancer types and shown to be organized into cancer cell states; however, it remains unclear to what extent these states span tumor types, constituting general features of cancer. Here, we perform a pan-cancer single-cell RNA-Seq analysis across 15 cancer types and identify a catalog of gene modules whose expression defines recurrent cancer cell states including ‘stress’, ‘interferon response’, ‘epithelial-mesenchymal transition’, ‘metal response’, ‘basal’ and ‘ciliated’. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL19057 GPL19415

31 Samples

Download data: CSV, H5, JPG, JSON, MTX, PNG, TSV