GEO DataSets

(Submitter supplied) Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction are still unfolding. By combining an acute depletion system with high resolution genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL30173

12 Samples

Download data: BW

(Submitter supplied) Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction are still unfolding. By combining an acute depletion system with high resolution genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30173

51 Samples

Download data

(Submitter supplied) Perineural invasion (PNI) is a unique biological feature of pancreatic cancer and is a key cause of pancreatic cancer metastasis, recurrence and poor postoperative survival, but its mechanism is largely unclarified. Clinical sample analysis and endoscopic ultrasonographic elasticity scoring indicated that cancer-associated fibroblasts (CAFs) are closely related to the occurrence of PNI. Furthermore, CAF-derived extracellular vesicles played an extremely important role in PNI in a dorsal root ganglion (DRG) coculture model and sciatic nerve model. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT

(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) Persistent inflammation driven by cytokines like type-one interferon (IFN-I) can cause immunosuppression. We show that administration of the JAK1 inhibitor itacitinib after anti-PD1 immunotherapy improves immune function and anti-tumor responses in mice, and results in high response rates (67%) in a phase-2 clinical trial for metastatic non-small cell lung cancer. Patients who failed to respond to initial anti-PD1 immunotherapy but responded after addition of itacitinib had multiple features of poor immune function to anti-PD1 alone that improved after JAK inhibition. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

79 Samples

Download data: RDS

(Submitter supplied) We assessed the chromatin localization of XPO1 and p300 in response to C646 (10 uM), S109 (1 uM), and SP100030 (1 uM). We used CUT&RUN sequencing as a lower-input (500,000 cells per sample), higher-sensitivity alternative to ChIP-Seq to assess chromatin binding of different factors

Organism:

Homo sapiens

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

20 Samples

Download data: BIGWIG

(Submitter supplied) High-throughput sequencing technologies have enabled many biological discoveries; nevertheless, the resolution of bulk RNA sequencing is insufficient to elucidate the heterogeneity at the single-cell level. Single-cell RNA sequencing (scRNA-Seq) has emerged as a powerful tool for disentangling this complexity.. A major challenge in scRNA-Seq of blood is the analysis of granulocytes. These cells are pivotal to immunological responses but are recalcitrant to isolation from blood without inducing activation artifacts, thereby perturbing their transcriptomic integrity.. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

7 Samples

Download data: RDS

(Submitter supplied) Keloids are scar tissue that can develop under tensile stress and manifest the tactile itch called alloknesis due to the heterogeneous course. But the molecular and cellular mechanisms underlying the pathology of keloid have been still unknown. Here, we found that unique fibroblast subpopulation that have dense-core granules with enhanced expression of PIEZO2 in the dermal layer of keloid tissue with alloknesis, a pressure-tactile itch. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

2 Samples

Download data: CSV

(Submitter supplied) Keloids are scar tissue that can develop under tensile stress and manifest the tactile itch called alloknesis due to the heterogeneous course. But the molecular and cellular mechanisms underlying the pathology of keloid have been still unknown. Here, we found that unique fibroblast subpopulation that have dense-core granules with enhanced expression of PIEZO2 in the dermal layer of keloid tissue with alloknesis, a pressure-tactile itch. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: MTX, TSV

(Submitter supplied) Histone modifications are typically recognized by chromatin-binding protein modules (referred to as “readers”) to mediate fundamental processes such as transcription. Lysine β-hydroxybutyrylation (Kbhb) is a new type of histone mark that couples metabolism to gene expression. However, the readers that prefer histone Kbhb remain elusive. This knowledge gap must be filled in order to reveal the molecular mechanism of this epigenetic regulation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

2 Samples

Download data: XLS

(Submitter supplied) Histone modifications are typically recognized by chromatin-binding protein modules (referred to as “readers”) to mediate fundamental processes such as transcription. Lysine β-hydroxybutyrylation (Kbhb) is a new type of histone mark that couples metabolism to gene expression. However, the readers that prefer histone Kbhb remain elusive. This knowledge gap must be filled in order to reveal the molecular mechanism of this epigenetic regulation. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

5 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Schizophrenia affects approximately 1% of the world population. Genetics, epigenetics, and environmental factors are known to play a role in this psychiatric disorder. While there is a high concordance in monozygotic twins, about half of twin pairs are discordant for schizophrenia. To address the question of how and when concordance in monozygotic twins occur, we have obtained fibroblasts from two pairs of schizophrenia discordant twins (one sibling with schizophrenia while the second one is unaffected by schizophrenia) and three pairs of healthy twins (both of the siblings are healthy). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

14 Samples

Download data: TXT

(Submitter supplied) We delved into the consequences of macrophages that co-cultured with PDAC cells with Vector/MLKL overexpression. We treated THP1 derived macrophages with PANC1 cells with Vector/MLKL overexpression.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: CSV

(Submitter supplied) In order to profile the translation events that were regulated by FBXO32, Ribo-seq was performed on PANC-1 cells which was used to generate FBXO32 stably depleted pancreatic cancer cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: TXT

(Submitter supplied) Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease due to gradual motorneurons (MN) degeneration. Among the processes associated to ALS pathogenesis, there is the formation of cytoplasmic inclusions produced by mutant protein aggregation, among which the RNA binding protein FUS. In this work we show that such inclusions are significantly reduced in number and dissolve faster when the RNA m6A content is diminished as a consequence of the m6A writer METTL3 knock-down. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

4 Samples

Download data: BED, BW

(Submitter supplied) Neutrophil extracellular traps (NETs) are a key antimicrobial feature of cellular innate immunity mediated by polymorphonuclear neutrophils (PMNs). NETs trap and kill microbes but have also been linked to inflammation in atherosclerosis, arthritis, or psoriasis by unknown mechanisms. We here report that NET-associated RNA (naRNA, which was RNA-sequenced from human primary neutrophil NETs here) stimulated further NET formation in naïve PMNs via a unique TLR8-NLRP3-caspase-1-gasdermin D-dependent inflammasome pathway. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: SF, TSV

(Submitter supplied) We delved into the consequences of METs formation. We treated wild-type PANC-1 with METs-containing CM and performed RNA-seq.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: XLSX

(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