GEO DataSets

(Submitter supplied) 3' based single-cell RNA sequencing (scRNA-seq) has enabled the study of gene expression at the individual cell level and the development of few methods to quantify transcriptomic variability at the single-cell level. Yet, most of these methods have low sensitivity and specificity. Here, we present SCALPEL, a new tool to quantify and characterize transcript isoforms at the single-cell level using standard 3' based single-cell transcriptomics data. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

2 Samples

Download data: MTX, TSV

(Submitter supplied) Ferroptosis is a unique iron-dependent form of non-apoptotic cell death characterized by devastating lipid peroxidation. Whilst growing evidence suggests that ferroptosis is a type of autophagy-dependent cell death, the underlying molecular mechanisms regulating ferroptosis are largely unknown. In this study, through an unbiased RNA-sequencing screening, we demonstrate the activation of a multi-faceted tumor-suppressor protein Par-4/PAWR during ferroptosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

6 Samples

Download data: TXT

(Submitter supplied) Vascular remodeling to match arterial diameter to tissue metabolic requirements commonly fails in ischemic disease. Endothelial cells (EC) sense fluid shear stress (FSS) from blood flow to maintain FSS within a narrow range in healthy vessels. Higher FSS induces vessel outward remodeling to return FSS to physiological levels, but mechanisms are poorly understood. We previously reported that Smad1/5 is maximally activated at physiological FSS and suppressed at higher flow. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

8 Samples

Download data: XLSX

(Submitter supplied) Extrachromosomal DNA (ecDNA) presents a major challenge for cancer patients. EcDNA renders tumours treatment-resistant by facilitating massive oncogene transcription and rapid genome evolution, contributing to poor patient survival. At present, there are no ecDNA-specific treatments. Here we show that enhancing transcription replication conflict enables targeted elimination of ecDNA-containing cancers. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL21697

42 Samples

Download data: BW

(Submitter supplied) Extrachromosomal DNA (ecDNA) presents a major challenge for cancer patients. EcDNA renders tumours treatment-resistant by facilitating massive oncogene transcription and rapid genome evolution, contributing to poor patient survival. At present, there are no ecDNA-specific treatments. Here we show that enhancing transcription replication conflict enables targeted elimination of ecDNA-containing cancers. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

8 Samples

Download data: BW

(Submitter supplied) Extrachromosomal DNA (ecDNA) presents a major challenge for cancer patients. EcDNA renders tumours treatment-resistant by facilitating massive oncogene transcription and rapid genome evolution, contributing to poor patient survival. At present, there are no ecDNA-specific treatments. Here we show that enhancing transcription replication conflict enables targeted elimination of ecDNA-containing cancers. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21697

16 Samples

Download data: BROADPEAK, BW

(Submitter supplied) As cancer immunotherapy and precision medicine dynamically evolve, there is greater need for pre-clinical models that can better replicate the intact tumor and its complex tumor microenvironment (TME). Precision-cut tumor slices (PCTS) have recently emerged as an ex vivo human tumor model, offering the opportunity to study individual patient responses to targeted therapies, including immunotherapies. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

26 Samples

Download data: XLSX

(Submitter supplied) We performed RNA-seq in TeloHAEC with samples where CALCRL was silenced using siRNA or enhancer-8 deleted using CRISPR-cas9 system to investigate the genes that are differentially expressed under CALCRL knockdown.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

14 Samples

Download data: TXT

(Submitter supplied) Drug-tolerance has emerged as one of the major non-genetic adaptive processes driving resistance to targeted therapy (TT) in non-small cell lung cancer (NSCLC). However, the kinetics and sequence of molecular events governing this adaptive response remain poorly understood. Here, we performed transcriptomic profiling by RNAseq in a panel of EGFR-mutant NSCLC cell lines (PC9, HCC4006, H3255 and HCC827) that were previously subcloned to minimize the presence of potential pre-existing resistant cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

44 Samples

Download data: TSV

(Submitter supplied) Drug-tolerance has emerged as one of the major non-genetic adaptive processes driving resistance to targeted therapy (TT) in non-small cell lung cancer (NSCLC). However, the kinetics and sequence of molecular events governing this adaptive response remain poorly understood. Here, we used the FUCCI (fluorescence ubiquitination cell cycle indicator) system to perform real-time monitoring of the cell cycle dynamics the EGFR-mutant NSCLC cell line HCC4006, which was previously subcloned to minimize the presence of potential pre-existing resistant cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

6 Samples

Download data: TSV

(Submitter supplied) Endothelial cells control inflammation in inflammatory and infectious diseases through regulating endothelial gene expression and permeability. Roundabout4 (Robo4) is an endothelial-specific protein that stabilizes endothelial cells. Robo4 has been shown to ameliorate mouse inflammatory and severe infectious diseases, such as sepsis and COVID-19 by reducing vascular permeability. Despite this, it remains uncertain whether these are the only mechanisms by which Robo4 ameliorates the diseases. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

12 Samples

Download data: TXT

(Submitter supplied) NAD besides its key role in cellular metabolism can serve as an alternative 5’ cap at several short non-coding RNAs. However, the function of the NAD cap remains elusive. Here, we investigate NAD capping of RNAs upon HIV-1 infection, which is associated with intracellular pellagra – depletion of NAD/NADH cellular pool. We applied NAD captureSeq on HIV-1 infected/noninfected cells and we revealed that four snRNAs (U1, U4ATAC, U5E and U7) and four snoRNAs (snord3G, snord102, snorA50A and snord3B) lost NAD cap upon HIV-1 infection. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL18573 GPL21697

22 Samples

Download data: TXT

(Submitter supplied) DNA replication progression can be affected by the presence of physical barriers on the DNA, like the RNA Polymerases, leading to replication stress and DNA damage. Nonetheless, we do not know the overall influence of transcription on DNA replication progression. To characterize what happens at sites where DNA replication forks stall and pause, we establish a genome-wide approach to identify them. This approach uses multiple timepoints to identify replication fork/stalling hotspots as the replication progresses through the genome. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

4 Samples

Download data: TXT

(Submitter supplied) Estrogen-receptor alpha (ERα)-dependent enhancers in the human breast cancer cell line MCF7 are a well-studied model system that allows high temporal resolution tracking of the different molecular events after hormone treatment and in which the enhancer and their target genes, as well as many of the molecular mechanisms operating in enhancer activation, are well defined. We use Capture-C to look at enhancer-promoter contact frequencies of GREB1 and NRIP1 genes across a time course (5, 30 and 60 min) after E2 addition to MCF7 cells which had been extensively starved of hormone. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL21697 GPL30173

46 Samples

Download data: MCOOL

(Submitter supplied) Estrogen-receptor alpha (ERα)-dependent enhancers in the human breast cancer cell line MCF-7 are a well-studied model system that allows high temporal resolution tracking of the different molecular events after hormone treatment and in which the enhancer and their target genes, as well as many of the molecular mechanisms operating in enhancer activation, are well defined. We use nascent RNA-seq (TT-seq) across a time course (5, 30 and 60 min) after E2 addition to MCF-7 cells which had been extensively starved of hormone to assess the transcription dynamics of E2-responsive genes and enhancers and to link this with other aspects of rapid gene activation under study, i.e. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

8 Samples

Download data: BW, TXT

(Submitter supplied) T cells are required for protective immunity against Mycobacterium tuberculosis. We recently described a cohort of Ugandan household contacts of tuberculosis cases who appear to “resist” M. tuberculosis infection (resisters; RSTRs) and showed that these individuals harbor IFN-γ–independent T cell responses to M. tuberculosis–specific peptide antigens. However, T cells also recognize nonprotein antigens via antigen-presenting systems that are independent of genetic background, known as donor-unrestricted T cells (DURTs). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

9 Samples

Download data: CSV, H5

(Submitter supplied) Transcription factors bind to sequence motifs and act as activators or repressors. Transcription factors interface with a constellation of accessory cofactors to regulate distinct mechanistic steps to regulate transcription. We rapidly degraded the essential and ubiquitously expressed transcription factor ZNF143 to determine its function in the transcription cycle. ZNF143 facilitates RNA Polymerase initiation and activates gene expression. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21697

8 Samples

Download data: BIGWIG

(Submitter supplied) Transcription factors bind to sequence motifs and act as activators or repressors. Transcription factors interface with a constellation of accessory cofactors to regulate distinct mechanistic steps to regulate transcription. We rapidly degraded the essential and ubiquitously expressed transcription factor ZNF143 to determine its function in the transcription cycle. ZNF143 facilitates RNA Polymerase initiation and activates gene expression. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

16 Samples

Download data: BED, BIGWIG

(Submitter supplied) Transcription factors bind to sequence motifs and act as activators or repressors. Transcription factors interface with a constellation of accessory cofactors to regulate distinct mechanistic steps to regulate transcription. We rapidly degraded the essential and ubiquitously expressed transcription factor ZNF143 to determine its function in the transcription cycle. ZNF143 facilitates RNA Polymerase initiation and activates gene expression. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

16 Samples

Download data: BED, BIGWIG

(Submitter supplied) We report the development of a method (nanoSPLITS) capable of performing global proteome and transcriptome measurements from the same single-cell.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

192 Samples

Download data: TXT