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Items: 1 to 20 of 749

1.

Genome-wide chromatin profiles of ZNF395

(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:
GPL16791 GPL20301
15 Samples
Download data: BED
Series
Accession:
GSE247118
ID:
200247118
2.

Genome-wide chromatin profiles of ZNF395 [ChIP-seq]

(Submitter supplied) Hypoxia signaling induced by VHL deficiency fuels growth but also poses immense metabolic stress to clear cell renal cell carcinomas (ccRCCs). Tumor cells depend on glutamine as the primary source of tricarboxylic acid (TCA) anaplerosis. Hypoxia-inducible factor alpha (HIFα) governs glycolysis but does not directly regulate glutamine metabolism; instead, the factor responsible for orchestrating glutamine metabolism and mitochondrial adaptations to hypoxia remains elusive. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16791
9 Samples
Download data: BED
Series
Accession:
GSE247116
ID:
200247116
3.

Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair

(Submitter supplied) Oncogene amplification on extrachromosomal DNA (ecDNA) is a pervasive driver event in cancer, yet our understanding of how ecDNA forms is limited. Here, we couple a CRISPR-based method for ecDNA induction with extensive characterization of newly formed ecDNA to examine their biogenesis. We find that DNA circularization is efficient, irrespective of 3D genome context, with formation of 800kb, 1 Mb, and 1.8 Mb ecDNAs reaching or exceeding 15%. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL21697
246 Samples
Download data: CSV
Series
Accession:
GSE273081
ID:
200273081
4.

Transcriptomic analysis of human naive B cells stimulated by CD40L, CpG, anti-IgM IgG, IL-4 or combinations

(Submitter supplied) B-lymphocytes play major adaptive immune roles, producing antibody and driving cell mediated responses. However, how B-cells acutely differentiate in response to receptor signaling codes, including T-cell dependent versus independent cues, remains incompletely understood. To gain insights, we used multi-omic profiling to characterize ex vivo primary human B-cell transcriptomic, proteomic and metabolomic remodeling by B-cell receptor (BCR), Toll-like receptor 9 (TLR9), CD40-ligand (CD40L), interleukin-4 (IL4) or combinations thereof, highlighting key stimulus-specific phenotypes.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
36 Samples
Download data: XLSX
Series
Accession:
GSE232769
ID:
200232769
5.

Opto-seq reveals input-specific immediate early gene induction in ventral tegmental area cell types

(Submitter supplied) The ventral tegmental area (VTA) is a critical node in circuits governing motivated behavior and is home to diverse populations of neurons that release dopamine, GABA, glutamate, or combinations of these neurotransmitters. The VTA receives inputs from many brain regions, but a comprehensive understanding of input-specific activation of VTA neuronal subpopulations is lacking. To address this, we combined optogenetic stimulation of select VTA inputs with single-nucleus RNA sequencing (snRNAseq) and highly multiplexed in situ hybridization to identify distinct neuronal clusters and characterize their spatial distribution and activation patterns. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21103
4 Samples
Download data: MTX, TSV
Series
Accession:
GSE235086
ID:
200235086
6.

Iterative deep learning-design of human enhancers exploits condensed sequence grammar to achieve cell type-specificity [scRNA-Seq]

(Submitter supplied) An important and largely unsolved problem in synthetic biology is how to target gene expression to specific cell types. Here, we apply iterative deep learning to design synthetic enhancers with strong differential activity between two human cell lines. We initially train models on published datasets of enhancer activity and chromatin accessibility and use them to guide the design of synthetic enhancers that maximize predicted specificity. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL34284
2 Samples
Download data: H5
Series
Accession:
GSE269037
ID:
200269037
7.

Functional characterization of a heat shock factor regulated enhancer at coronary artery disease associated locus that controls CALCRL expression in endothelial cells

(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
Series
Accession:
GSE222118
ID:
200222118
8.

Insights into selective action of microsecond pulsed electric fields on healthy and cancer stem cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL23159
16 Samples
Download data: CEL
Series
Accession:
GSE248601
ID:
200248601
9.

Insights into selective action of microsecond pulsed electric fields on healthy and cancer stem cells (NHA)

(Submitter supplied) In the last few years, pulsed electric fields have emerged as promising clinical tools for tumor treatments. This study highlights the distinct impact of a specific pulsed electric field protocol named PEF-5 (0.3 MV/m, 40 µs, 5 pulses) on astrocytes (NHA), medulloblastoma (D283) and gli-oblastoma (U87 NS) cancer stem-like cells. We pursued this goal performing ultrastructural analyses corroborated by molecular/omics approaches to understand the vulnerability or re-sistance mechanisms triggered by PEF-5 exposure in the different cell types. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL23159
8 Samples
Download data: CEL
Series
Accession:
GSE248600
ID:
200248600
10.

Insights into selective action of microsecond pulsed electric fields on healthy and cancer stem cells (D283)

(Submitter supplied) In the last few years, pulsed electric fields have emerged as promising clinical tools for tumor treatments. This study highlights the distinct impact of a specific pulsed electric field protocol named PEF-5 (0.3 MV/m, 40 µs, 5 pulses) on astrocytes (NHA), medulloblastoma (D283) and gli-oblastoma (U87 NS) cancer stem-like cells. We pursued this goal performing ultrastructural analyses corroborated by molecular/omics approaches to understand the vulnerability or re-sistance mechanisms triggered by PEF-5 exposure in the different cell types. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL23159
8 Samples
Download data: CEL
Series
Accession:
GSE248599
ID:
200248599
11.

Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data

(Submitter supplied) Unraveling the transcriptional programs that control how cells divide, differentiate, and respond to their environments requires a precise understanding of transcription factors'(TFs) DNA-binding activities. Calling cards (CC) technology uses transposons to capture transient TF binding event at one instant in time and then read them out at a later time. This methodology can also be used to simultaneously measure transcription factor binding and mRNA expression from single cells CC and to record and integrate TF binding events across time in any cell type of interest without the need for purification. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL24676
22 Samples
Download data: TXT
Series
Accession:
GSE248420
ID:
200248420
12.

The meningeal transciptional response to traumatic brain injury and aging

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL21103 GPL19057
14 Samples
Download data: MTX, TSV
Series
Accession:
GSE206941
ID:
200206941
13.

The meningeal transciptional response to traumatic brain injury and aging [scRNA-seq]

(Submitter supplied) Emerging evidence suggests that the meningeal compartment plays instrumental roles in various neurological disorders and can modulate neurodevelopment and behavior. While this has sparked great interest in the meninges, we still lack fundamental knowledge about meningeal biology. Here, we utilized high-throughput RNA sequencing (RNA-seq) techniques to investigate the transcriptional response of the meninges to traumatic brain injury (TBI) and aging in the sub-acute and chronic time frames. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
2 Samples
Download data: MTX, TSV
Series
Accession:
GSE206940
ID:
200206940
14.

GDF15 Secretion is Increased in Resposne to Skeletal Muscle Contraction and Potentiates Glucose-Stimulated Insulin Release in Pancreatic β-cells 

(Submitter supplied) Lifestyle intervention including exercise restores glucose homeostasis and pancreatic β-cell function in type 2 diabetes (T2D). However, exercise compliance is a challenge. Novel alternative or adjuvant approaches are necessary. During exercise, the contracting skeletal muscle acts as endocrine organ via the secretion and endocrine signaling of functional proteins. We postulated that contracting skeletal muscle secretes proteins that target pancreatic β-cells and regulate insulin secretion and glucose metabolism. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
16 Samples
Download data: TXT
Series
Accession:
GSE139872
ID:
200139872
15.

Integrative CUT&Tag/RNA-Seq analysis of histone variant macroH2A1-dependent orchestration of human iPSCs reprogramming

(Submitter supplied) Human-induced pluripotent stem cells (iPSCs) can be derived from adult stem cells by forced expression of defined transcription factors. This paves the way for autologous iPSC-derived therapies, which, however, are not yet considered safe. Moreover, reprogramming of somatic cells into iPSCs is an inefficient process, in the range of 0.1%–1%. The epigenetic mechanisms implicated in iPSCs reprogramming are not well understood. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16791
8 Samples
Download data: BW
Series
Accession:
GSE214013
ID:
200214013
16.

Real-time quantitative PCR analysis of Nannochloropsis gaditana

(Submitter supplied) Nannochloropsis gaditana cells were cultivated under continuous light as a control condition versus 3 different flashing light conditions (FL5, FL50 and FL500). This study is complementary to Lima et al. (2020) where physiology and photosynthetic capacity were assesed. Here we analyzed the mRNA expression level of key genes related to photoshynthesis, lipid and starch synthesis, and nitrogen assimilation. more...
Organism:
Nannochloropsis gaditana
Type:
Expression profiling by RT-PCR
Platform:
GPL32525
4 Samples
Download data: XLS
Series
Accession:
GSE210188
ID:
200210188
17.

DUX4 is a multifunctional factor priming human embryonic genome activation

(Submitter supplied) Double homeobox 4 (DUX4) is expressed in at the early preimplantation stage in human embryos. Here we show that induced human DUX4 expression substantially alters the non-coding chromatin accessibility of non-coding DNA and activates thousands of newly identified putative transcribed enhancer-like regions, preferentially located within ERVL-MaLR repeat elements. CRISPR activation of transcribed enhancers by C-terminal DUX4 motifs results in the increased expression of target embryonic genome activation (EGA) genes ZSCAN4 and KHDC1P1. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL21697 GPL18573
40 Samples
Download data: BED, CSV
18.

Gene expression profiling of teloHAEC cells with CRISPR-Cas9-mediated deletion of candidate enhancer regions

(Submitter supplied) Functional consequences of genetic variation in the non-coding human genome are difficult to ascertain despite demonstrated associations to common, complex disease traits. To elucidate properties of functional non-coding SNPs with effects in human endothelial cells (EC), we utilized our previous molecular Quantitative Trait Locus (molQTL) analysis for transcription factor binding, chromatin accessibility, and H3K27 acetylation to nominate a set of likely functional non-coding SNPs. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
27 Samples
Download data: TXT
Series
Accession:
GSE191253
ID:
200191253
19.

Massively parallel profiling of human regulatory variants in endothelial cells

(Submitter supplied) Genome-wide association studies (GWAS-s) have linked thousands of genetic variants with complex diseases and traits. However, most genetic variants identified reside in non-coding regions of the genome making it hard to predict and understand the molecular mechanisms underlying causal alleles. We have previously performed molecular Quantitative Trait Locus (molQTL) analysis for transcription factor binding, chromatin accessibility, and H3K27 acetylation across primary Human Aortic Endothelial Cell (HAEC) samples. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
12 Samples
Download data: TXT
20.

Effect of nanosecond pulsed electric field (nsPEF) on gene expression in TM3 Leydig cells

(Submitter supplied) The aim of our study was to analyze cell response to nanosecond pulsed electric field (nsPEF) at the gene expression level. TM3 Leydig cells were used as a model. Transcriptomics analysis was carried out immediately after exposure (0 h) and 4 or 24 h after treatment.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL21163
24 Samples
Download data: TXT
Series
Accession:
GSE155355
ID:
200155355
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