l glutamine - GEO DataSets

Select item 2002814361.

Loss of SMARCB1 evokes targetable epigenetic vulnerabilities in Epithelioid Sarcoma [ChIP-Seq]

(Submitter supplied) Dysfunction of epigenetic modulators such as the SWI/SNF complex is involved in a wide spectrum of cancer entities, yet their precise role in carcinogenesis is not clear to date Among SWI/SNF-mutant entities, SMARCB1-deficient cancers such as Epithelioid Sarcoma (EpS) are characterized by this genetic event in an otherwise rather silent mutational landscape. However, its oncogenic role remains unclear. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL24676
24 Samples

Download data: BED

Series

Accession:: GSE281436

ID:: 200281436

Select item 2002814342.

Loss of SMARCB1 evokes targetable epigenetic vulnerabilities in Epithelioid Sarcoma [ATAC-Seq]

(Submitter supplied) Dysfunction of epigenetic modulators such as the SWI/SNF complex is involved in a wide spectrum of cancer entities, yet their precise role in carcinogenesis is not clear to date Among SWI/SNF-mutant entities, SMARCB1-deficient cancers such as Epithelioid Sarcoma (EpS) are characterized by this genetic event in an otherwise rather silent mutational landscape. However, its oncogenic role remains unclear. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL24676
24 Samples

Download data: BED

Series

Accession:: GSE281434

ID:: 200281434

Select item 2001884873.

Treatment-associated gene expression in hematopoietic stem/progenitor cells from patients with polycythemia vera (PV) [6 hour treatment]

(Submitter supplied) The objective of the study was to assess gene expression changes in CD34+ hematopoietic stem/progenitor cells from PV patients upon ex vivo treatment with clusterin (CLU), IKK-16, their combination, with hydroxyurea (HU) or with solvent control.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
23 Samples

Download data: TXT

Series

Accession:: GSE188487

ID:: 200188487

Select item 2002728494.

EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling

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

Organism:: Mus musculus

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

Platform:: GPL24247
119 Samples

Download data: BIGWIG, TAB

Series

Accession:: GSE272849

ID:: 200272849

Select item 2002725495.

EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [ChIP-Seq]

(Submitter supplied) In this study we analysed the dynamic changes in the epigenetic landscape during first embryonic lineage decision following pluripotency exit. Here, mouse pluripotent epiblast cells segregate towards mesoderm and endoderm (ME) or neuroectoderm (NE). The analysis of chromatin accessibility, histone modifications and accompanied gene expression confirmed a bias of the epigenetic landscape towards NE fate while ME cis regulatory elements (CREs) are becoming accessible and active during lineage specification. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL24247
40 Samples

Download data: BIGWIG

Series

Accession:: GSE272549

ID:: 200272549

Select item 2002725476.

EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [RNA-Seq]

(Submitter supplied) In this study we analysed the dynamic changes in the epigenetic landscape during first embryonic lineage decision following pluripotency exit. Here, mouse pluripotent epiblast cells segregate towards mesoderm and endoderm (ME) or neuroectoderm (NE). The analysis of chromatin accessibility, histone modifications and accompanied gene expression confirmed a bias of the epigenetic landscape towards NE fate while ME cis regulatory elements (CREs) are becoming accessible and active during lineage specification. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24247
49 Samples

Download data: TAB, XLSX

Series

Accession:: GSE272547

ID:: 200272547

Select item 2002725457.

EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [ATAC-Seq]

(Submitter supplied) In this study we analysed the dynamic changes in the epigenetic landscape during first embryonic lineage decision following pluripotency exit. Here, mouse pluripotent epiblast cells segregate towards mesoderm and endoderm (ME) or neuroectoderm (NE). The analysis of chromatin accessibility, histone modifications and accompanied gene expression confirmed a bias of the epigenetic landscape towards NE fate while ME cis regulatory elements (CREs) are becoming accessible and active during lineage specification. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL24247
30 Samples

Download data: BIGWIG

Series

Accession:: GSE272545

ID:: 200272545

Select item 2002533548.

Distinct pathways for removal of defective RNA polymerase II transcription complexes at a promoter-proximal pause checkpointm [RN21236 dTAG TTchem-seq]

(Submitter supplied) The purpose and function of Integrator and RNA polymerase II (RNAPII) promoter-proximal pausing remain uncertain. Here, we show that when Integrator function is compromised by loss of INTS6, RNAPII interacts increasingly with proteins from alternative pathways for its DNA dissociation, including CUL3-ARMC5 (CRL3ARMC5), which ubiquitylates Ser5-phosphorylated Rpb1 and targets it for degradation. ARMC5-dependent RNAPII ubiquitylation is activated by defects in factors required for correctly regulated promoter-proximal pausing, including Integrator, DSIF and mRNA capping enzyme. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL20301
6 Samples

Download data: BIGWIG

Series

Accession:: GSE253354

ID:: 200253354

Select item 2002479599.

Ldha positively regulates the lactylation of Hdac1 to hinder the 2-cell state of embryonic stem cells [RNA-seq]

(Submitter supplied) Protein lactylation is a process that is fueled by lactate, generated by the enzyme lactate dehydrogenase (Ldh) from pyruvate. Despite prior research, the precise role of protein lactylation in controlling the identity of mouse embryonic stem cells (ESCs) is still not fully understood. We observed that inhibiting or eliminating Ldha causes a reduction in global protein lactylation in ESCs, and RNA-seq analysis suggests that Ldha inhibition induces a 2-cell-like cell (2CLC) signature in ESCs. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24247
4 Samples

Download data: TXT

Series

Accession:: GSE247959

ID:: 200247959

Select item 20024795810.

Ldha positively regulates the lactylation of Hdac1 to hinder the 2-cell state of embryonic stem cells [ChIP-seq]

(Submitter supplied) Protein lactylation is a process that is fueled by lactate, generated by the enzyme lactate dehydrogenase (Ldh) from pyruvate. Despite prior research, the precise role of protein lactylation in controlling the identity of mouse embryonic stem cells (ESCs) is still not fully understood. We observed that inhibiting or eliminating Ldha causes a reduction in global protein lactylation in ESCs, and RNA-seq analysis suggests that Ldha inhibition induces a 2-cell-like cell (2CLC) signature in ESCs. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL24247
3 Samples

Download data: BW

Series

Accession:: GSE247958

ID:: 200247958

Select item 20024410211.

Role of Mac1 in gene regulation under copper limiting conditions in Fusarium oxysporum [ChIP-seq]

(Submitter supplied) The transcription factor Mac1 is a key regulator of copper homeostasis and controls the transcriptional response to copper-limiting conditions in fungi. Expression analyses performed in the soil-borne plant pathogen Fusarium oxysporum revealed that almost all copper starvation-induced genes are downregulated in the absence of the regulator Mac1. The aim of this ChIP-seq analysis is to elucidate which of these genes are direct targets of Mac1.

Organism:: Fusarium oxysporum f. sp. lycopersici 4287

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL33791
9 Samples

Download data: WIG

Series

Accession:: GSE244102

ID:: 200244102

Select item 20024324712.

Effect of Mac1 deletion on copper homoestasis and virulence in Fusarium oxysporum f. sp. lycopersici [RNA-seq]

(Submitter supplied) The transcription factor Mac1 is a key regulator of copper homeostasis, controlling the transcriptional response to copper-limiting conditions in fungi. It has been described as a virulence factor in human pathogens such as Candida albicans and Aspergillus fumigatus, but surprisingly its role in plant pathogenesis is poorly understood. Targeted deletion of Mac1 in the soilborne pathogen Fusarium oxisporum results in an inability to grow under copper-limited conditions and kills tomato plants. more...

Organism:: Fusarium oxysporum f. sp. lycopersici 4287

Type:: Expression profiling by high throughput sequencing

Platform:: GPL33765
24 Samples

Download data: SF

Series

Accession:: GSE243247

ID:: 200243247

Select item 20018280413.

DDX18 coordinates nucleolus phase separation and chromatin organization to control the pluripotency of human embryonic stem cells.

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

Organism:: Homo sapiens

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

Platform:: GPL16791
10 Samples

Download data: TDF

Series

Accession:: GSE182804

ID:: 200182804

Select item 20018280214.

DDX18 coordinates nucleolus phase separation and chromatin organization to control the pluripotency of human embryonic stem cells [RNA-seq]

(Submitter supplied) Pluripotent stem cells are unique in their large nucleus and manifestly open chromatin structure with hypertranscriptional activities. How the nucleolus, the largest membraneless and phase-separated subnuclear organelle, maintains its structural integrity in pluripotency maintenance remains incompletely understood. By studying nucleolus-specific DEAD-box RNA helicase-18 (DDX18) in human embryonic stem cells, we discover mechanisms controlling nucleolus phase separation and chromatin organization.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
6 Samples

Download data: TXT

Series

Accession:: GSE182802

ID:: 200182802

SRA Run Selector

Select item 20018280115.

DDX18 coordinates nucleolus phase separation and chromatin organization to control the pluripotency of human embryonic stem cells [DDX18_iCLIP-seq]

(Submitter supplied) Pluripotent stem cells are unique in their large nucleus and manifestly open chromatin structure with hypertranscriptional activities. How the nucleolus, the largest membraneless and phase-separated subnuclear organelle, maintains its structural integrity in pluripotency maintenance remains incompletely understood. By studying nucleolus-specific DEAD-box RNA helicase-18 (DDX18) in human embryonic stem cells, we discover mechanisms controlling nucleolus phase separation and chromatin organization.

Organism:: Homo sapiens

Type:: Other

Platform:: GPL16791
2 Samples

Download data: TXT

Series

Accession:: GSE182801

ID:: 200182801

SRA Run Selector

Select item 20018280016.

DDX18 coordinates nucleolus phase separation and chromatin organization to control the pluripotency of human embryonic stem cells [DDX18_CHIP-seq]

(Submitter supplied) Pluripotent stem cells are unique in their large nucleus and manifestly open chromatin structure with hypertranscriptional activities. How the nucleolus, the largest membraneless and phase-separated subnuclear organelle, maintains its structural integrity in pluripotency maintenance remains incompletely understood. By studying nucleolus-specific DEAD-box RNA helicase-18 (DDX18) in human embryonic stem cells, we discover mechanisms controlling nucleolus phase separation and chromatin organization.

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL16791
2 Samples

Download data: TDF

Series

Accession:: GSE182800

ID:: 200182800

SRA Run Selector

Select item 20028124217.

Decoupling the Biochemical and Mechanical Effects of Muscle Exercise on Motor Neurons with 2.5D Actuating Matrices

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

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL13112 GPL21103
38 Samples

Download data

Series

Accession:: GSE281242

ID:: 200281242

Select item 20028124118.

Decoupling the Biochemical and Mechanical Effects of Muscle Exercise on Motor Neurons with 2.5D Actuating Matrices [240614Ram_RNA-seq]

(Submitter supplied) We wanted to query the differences and similarities between our wild-type C2C12 cell line and our optogenetic ChR2 C2C12 myoblasts on the same day of differentiation. After 6 days on muscle differentiation medium, we extracted the RNA and sequenced it for 6 wells each.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21103
12 Samples

Download data: TSV

Series

Accession:: GSE281241

ID:: 200281241

Select item 20028068119.

The responses of CHA0 treated with WT(Col-0) root exudates, Gln and sgn3 myb36 root exudates

(Submitter supplied) In our previous work, we found that the root exudates of sgn3 myb36 promoted the colonization of CHA0 on roots. Through LC-MS, we identified a large amount of glutamine (Gln) in the root exudates of sgn3 myb36. Therefore, we aim to use RNA-seq to uncover whether the root exudates of sgn3 myb36 and Gln have the same regulatory effects on CHA0. By conducting differential analysis with the CK (CHA0 treated with wild-type root exudates), we hope to identify the specific regulatory mechanisms of sgn3 myb36 and Gln on CHA0.

Organism:: Pseudomonas protegens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL35063
9 Samples

Download data: CSV

Series

Accession:: GSE280681

ID:: 200280681

Select item 20027676920.

Prenatal dexamethasone exposure modificates H3K9me2 at the Mkp-1 locus in bone marrow osteoprogenitors

(Submitter supplied) Prenatal dexamethasone exposure (PDE) has long-term consequences in bone development. we investigated how PDE exerts persistent effect on bone metabolism in mouse offspring. Our results showed that PDE offspring exhibited reduced bone mass, fewer osteoblasts and diminished osteoprogenitors proliferation.And PDE increased MKP-1 expression, while decreasing H3 lysine 9 dimethylation (H3K9me2) at Mkp-1 gene locus. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL24247
6 Samples

Download data: BW

Series

Accession:: GSE276769

ID:: 200276769

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