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Items: 1 to 20 of 12611

1.

CLIP-seq analysis of WT and Gag chimera HIV-1 virions 3

(Submitter supplied) To investigate how the major HIV-1 structural protein Gag packages viral genomes efficiently, we replaced the NC domain of Gag with RNA binding domains from heterologous cellular RNA binding proteins to generate Gag chimeras. We hypothesize that the Gag chimeras that preferentially bind to purine-rich RNA sequences will package viral genomes efficiently. We performed CLIP-seq to identify the RNA sequences bound by WT Gag and Gag chimeras in cells, at the plasma membrane, and in virions.
Organism:
Homo sapiens
Type:
Other
Platform:
GPL18573
20 Samples
Download data: TXT
Series
Accession:
GSE281424
ID:
200281424

2.

CLIP-seq analysis of WT and Gag chimera HIV-1 virions 2

(Submitter supplied) To investigate how the major HIV-1 structural protein Gag packages viral genomes efficiently, we replaced the NC domain of Gag with RNA binding domains from heterologous cellular RNA binding proteins to generate Gag chimeras. We hypothesize that the Gag chimeras that preferentially bind to purine-rich RNA sequences will package viral genomes efficiently. We performed CLIP-seq to identify the RNA sequences bound by WT Gag and Gag chimeras in cells, at the plasma membrane, and in virions.
Organism:
Homo sapiens
Type:
Other
Platform:
GPL18573
37 Samples
Download data: TXT
Series
Accession:
GSE281423
ID:
200281423

3.

CLIP-seq analysis of WT and Gag chimera HIV-1 virions 1

(Submitter supplied) To investigate how the major HIV-1 structural protein Gag packages viral genomes efficiently, we replaced the NC domain of Gag with RNA binding domains from heterologous cellular RNA binding proteins to generate Gag chimeras. We hypothesize that the Gag chimeras that preferentially bind to purine-rich RNA sequences will package viral genomes efficiently. We performed CLIP-seq to identify the RNA sequences bound by WT Gag and Gag chimeras in cells, at the plasma membrane, and in virions.
Organism:
Homo sapiens
Type:
Other
Platform:
GPL18573
49 Samples
Download data: TXT
Series
Accession:
GSE281422
ID:
200281422

4.

A decision-point between programmed cell death and transdifferentiation in pancreatic cancer

(Submitter supplied) Transdifferentiation and changes of cellular identity are hallmarks of malignant transformation1-3. As such, the process of acinar-to-ductal metaplasia (ADM) represents a fundamental step in pancreatic ductal adenocarcinoma (PDAC) development, but regulatory pathways controlling ADM are not fully understood4,5. Here, we show that murine pancreatic acinar cells upregulate expression of CASPASE3, CASPASE8, RIPK3 and MLKL - key molecules driving both apoptosis and necroptosis6,7 - during transdifferentiation towards a duct-like phenotype. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
2 Samples
Download data: TSV
Series
Accession:
GSE223135
ID:
200223135

5.

A decision-point between programmed cell death and transdifferentiation in pancreatic cancer

(Submitter supplied) Mecanism of action of TAK inhibitor on immune cells and cancer cells extracted from pancreatic tumor (PDAC)
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
1 Sample
Download data: CSV
Series
Accession:
GSE275488
ID:
200275488

6.

Paired CRISPR screens to map gene regulation in cis and trans

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Other; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18573 GPL24676
42 Samples
Download data: TXT
Series
Accession:
GSE255701
ID:
200255701

7.

Paired CRISPR screens to map gene regulation in cis and trans (CUT&RUN)

(Submitter supplied) In this study, we develop a scalable approach that pairs discovery of cis- and trans-acting elements to systematically decipher the gene regulatory network. We explore the regulation of the immune checkpoint PD-L1 under both basal and IFNγ-stimulated contexts. PD-L1 expression on tumor cells serves as a clinically-actionable diagnostic for immune checkpoint blockade therapy across multiple cancer types.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
12 Samples
Download data: BW, NARROWPEAK
Series
Accession:
GSE255699
ID:
200255699

8.

Paired CRISPR screens to map gene regulation in cis and trans (ATAC-seq)

(Submitter supplied) In this study, we develop a scalable approach that pairs discovery of cis- and trans-acting elements to systematically decipher the gene regulatory network. We explore the regulation of the immune checkpoint PD-L1 under both basal and IFNγ-stimulated contexts. PD-L1 expression on tumor cells serves as a clinically-actionable diagnostic for immune checkpoint blockade therapy across multiple cancer types.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
18 Samples
Download data: BW, NARROWPEAK
Series
Accession:
GSE255698
ID:
200255698

9.

LncRNA adapters determine SWI/SNF complex occupancy at gene regulatory elements [CUT&Run]

(Submitter supplied) The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a key role in regulating gene expression in a context-dependent manner. SWI/SNF actively maintains open chromatin states across the genome and responds dynamically to cellular signals. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
5 Samples
Download data: BW
Series
Accession:
GSE278389
ID:
200278389

10.

LncRNA adapters determine SWI/SNF complex occupancy at gene regulatory elements [ATAC-Seq]

(Submitter supplied) The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a key role in regulating gene expression in a context-dependent manner. SWI/SNF actively maintains open chromatin states across the genome and responds dynamically to cellular signals. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
8 Samples
Download data: BW
Series
Accession:
GSE278388
ID:
200278388

11.

PTEN depletion reduces global levels of H3K27me3 to promote epithelial-to-mesenchymal transition in epithelial colorectal cancer cells [RNA-seq]

(Submitter supplied) Epithelial-to-mesenchymal (EMT) transition is one of the best-known examples of tumor cell plasticity. EMT enhances cancer cell metastasis, which is the main cause of colorectal cancer (CRC)-related mortality. Therefore, understanding underlying molecular mechanisms contributing to the EMT process is crucial to finding druggable targets and more effective therapeutic approaches in CRC. In this study, we demonstrated that activation of AKT induces EMT in epithelial CRC. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
12 Samples
Download data: CSV
Series
Accession:
GSE268979
ID:
200268979

PubMed

12.

PTEN depletion reduces global levels of H3K27me3 to promote epithelial-to-mesenchymal transition in epithelial colorectal cancer cells [ATAC-seq]

(Submitter supplied) Epithelial-to-mesenchymal (EMT) transition is one of the best-known examples of tumor cell plasticity. EMT enhances cancer cell metastasis, which is the main cause of colorectal cancer (CRC)-related mortality. Therefore, understanding underlying molecular mechanisms contributing to the EMT process is crucial to finding druggable targets and more effective therapeutic approaches in CRC. In this study, we demonstrated that activation of AKT induces EMT in epithelial CRC. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
8 Samples
Download data: NARROWPEAK
Series
Accession:
GSE268978
ID:
200268978

PubMed

13.

LncRNA adapters determine SWI/SNF complex occupancy at gene regulatory elements

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL30173 GPL18573
79 Samples
Download data: BW
Series
Accession:
GSE262070
ID:
200262070

14.

LncRNA adapters determine SWI/SNF complex occupancy at gene regulatory elements [iCLIP]

(Submitter supplied) The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a key role in regulating gene expression in a context-dependent manner. SWI/SNF actively maintains open chromatin states across the genome and responds dynamically to cellular signals. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL18573
5 Samples
Download data: BED
Series
Accession:
GSE262068
ID:
200262068

15.

LncRNA adapters determine SWI/SNF complex occupancy at gene regulatory elements [RedChIP]

(Submitter supplied) The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a key role in regulating gene expression in a context-dependent manner. SWI/SNF actively maintains open chromatin states across the genome and responds dynamically to cellular signals. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL18573
2 Samples
Download data: TXT
Series
Accession:
GSE262066
ID:
200262066

16.

LncRNA adapters determine SWI/SNF complex occupancy at gene regulatory elements [RIP-seq]

(Submitter supplied) The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a key role in regulating gene expression in a context-dependent manner. SWI/SNF actively maintains open chromatin states across the genome and responds dynamically to cellular signals. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL18573
6 Samples
Download data: BW
Series
Accession:
GSE262063
ID:
200262063

17.

LncRNA adapters determine SWI/SNF complex occupancy at gene regulatory elements [CutAndRun_PROTAC]

(Submitter supplied) The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a key role in regulating gene expression in a context-dependent manner. SWI/SNF actively maintains open chromatin states across the genome and responds dynamically to cellular signals. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
15 Samples
Download data: BW
Series
Accession:
GSE262059
ID:
200262059

18.

LncRNA adapters determine SWI/SNF complex occupancy at gene regulatory elements [ATAC-seq]

(Submitter supplied) The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a key role in regulating gene expression in a context-dependent manner. SWI/SNF actively maintains open chromatin states across the genome and responds dynamically to cellular signals. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
12 Samples
Download data: BW
Series
Accession:
GSE262057
ID:
200262057

19.

Patient-derived lymphomoids preserve the tumor architecture and allow testing response to therapies in lymphoma [Spatial Transcriptomics]

(Submitter supplied) We designed an ex vivo system to culture tissue explants from lymphoma tissue. To characterize the spatial and molecular structure of human lymphomoids and their tissue of origin, we performed spatial transcriptomics analyses on original tissues and lymphomoids obtained from 2 patients using the 10x Genomics Visium technology.
Organism:
Homo sapiens
Type:
Other
Platform:
GPL18573
5 Samples
Download data: H5, TAR
Series
Accession:
GSE269695
ID:
200269695

20.

C9orf72 expansion creates the unstable folate-sensitive fragile site FRA9A

(Submitter supplied) The hyper-unstable Chr9p21 locus, harbouring the interferon gene cluster, oncogenes and C9orf72, is linked to multiple diseases. C9orf72 (GGGGCC)n expansions (C9orf72Exp) are associated with incompletely penetrant amyotrophic lateral sclerosis, frontotemporal dementia and autoimmune disorders. C9orf72Exp patients display hyperactive cGAS-STING-linked interferon immune and DNA damage responses, but the source of immuno-stimulatory or damaged DNA is unknown. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
8 Samples
Download data: SF
Series
Accession:
GSE262674
ID:
200262674

PubMed

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