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GEO DataSets

Functional Genomics Studies

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Select item 2002941611.

PLAMseq enables the simultaneous proteo-genomic characterization of chromatin-associated proteins and protein interactions in a single workflow.

(Submitter supplied) Chromatin Immunoprecipitation (ChIP) and Co-Immunoprecipitation (CoIP) assays are the most common approaches to characterize the genomic localization and protein interactors, respectively for a protein of interest. However, these approaches require the use of specific antibodies, which are costly reagents that often face sensitivity and specificity issues. Based on TurboID, we developed PLAMseq (Proximity Labelled Affinity-purified Mass spectrometry plus sequencing), after a short biotin pulse, DNA-protein crosslinks are induced by formaldehyde and the interactors of a protein of interest together with their associated DNA sequences are purified simultaneously and identified by mass spectrometry-based proteomics and Next Generation Sequencing, respectively. more...

Organism:: Homo sapiens

Type:: Other

Platforms:: GPL24676 GPL18573
39 Samples

Download data: BIGWIG, BW

Series

Accession:: GSE294161

ID:: 200294161

Select item 2003031262.

Inhibition of heme biosynthesis triggers cuproptosis in acute myeloid leukemia

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

Organism:: Mus musculus; Homo sapiens

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

Platforms:: GPL19057 GPL18573
30 Samples

Download data

Series

Accession:: GSE303126

ID:: 200303126

Select item 2003082373.

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity V

(Submitter supplied) To assess genome-wide off-target activity of base editors and Cas9 nucleases identified by CHANGE-seq-BE, Digenome-seq, and CHANGE-seq, we performed hybrid capture sequencing for five therupatic loci (B2M, CBLB, CD7, CIITA, PDCD1) in human primary T-cells and PCSK9 in human hepatocytes. We observed high on-target editing for ABE, CBE, Cas9 mRNA edited cells and potential off-targets confirmed by hybrid capture sequencing. more...

Organism:: Homo sapiens

Type:: Other

Platforms:: GPL18573 GPL34281
36 Samples

Download data: CSV

Series

Accession:: GSE308237

ID:: 200308237

Select item 2003077404.

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity III

(Submitter supplied) To assess CHANGE-seq-BE performance, we used it to characterize ABE8e-NRCH base editor activity targeting sickle mutation (HBBS) in the HBB gene and identified additional 29 (53% more) bona fide off-targets than CIRCLE-seq. Furthermore, CHANGE-seq-BE applied for ABE8e targeting five therapeutically relevant loci (B2M, CBLB, CD7, CIITA, and PDCD1) in human primary T-cells and compared with Digenome-seq. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL18573
18 Samples

Download data: XLSX

Series

Accession:: GSE307740

ID:: 200307740

Select item 2002985345.

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity II

(Submitter supplied) To adapt and apply for cytosone base editors (CBEs), we perfomed CHANGE-seq-BE using eA3A-BE3 to target B2M, CBLB, CD7, CIITA and PDCD1 regions at different loci. CHANGE-seq-BE identified low frequency off-target editing rates ranging from 1.7% to 7.5% that are not identified by Digenome-seq further implies CHANGE-seq-BE is highly sensitive and can identify true off-targets while requiring 20-fold fewer sequencing reads.

Organism:: Homo sapiens

Type:: Other

Platform:: GPL18573
12 Samples

Download data: CSV

Series

Accession:: GSE298534

ID:: 200298534

Select item 2002984656.

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity I

(Submitter supplied) By CHANGE-seq-BE, we identified a total of 81 potential off-targets and confirmed 95.4% frequencies of on-target editing with no evident off-targets above the detection threshold compared to controls (rhAmp-seq, IDT).

Organism:: Homo sapiens

Type:: Other

Platform:: GPL18573
3 Samples

Download data: TSV

Series

Accession:: GSE298465

ID:: 200298465

Select item 2002701697.

GAPDH Controls Transcript Stability, Protein Translation and Drives Proliferation in Acute Myeloid Leukemia [GAPDH_KD_RNAseq]

(Submitter supplied) Dysregulation of RNA binding proteins (RBPs) is a hallmark in cancerous cells. In acute myeloid leukemia (AML) RBPs are key regulators of tumor proliferation. While classical RBPs have defined RNA binding domains, RNA recognition and function in AML by non-canonical RBPs (ncRBPs) remains unclear. Given the inherent complexity of targeting AML broadly, our goal was to uncover potential ncRBP candidates critical for AML survival using a CRISPR/Cas-based screening. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
12 Samples

Download data: TSV

Series

Accession:: GSE270169

ID:: 200270169

Select item 2002701688.

GAPDH Controls Transcript Stability, Protein Translation and Drives Proliferation in Acute Myeloid Leukemia [CLIP-seq]

Organism:: Homo sapiens

Type:: Other

Platform:: GPL18573
6 Samples

Download data: TSV

Series

Accession:: GSE270168

ID:: 200270168

Select item 2002505159.

GLIS3 RNA-seq

(Submitter supplied) Define the transcriptome of fibroblasts perturbed for GLIS3 in response to fibrotic stimuli.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
48 Samples

Download data: TSV

Series

Accession:: GSE250515

ID:: 200250515

Select item 20030377710.

Single-cell RNA-seq of nevus-derived melanocytes and matching perilesional skin melanocytes

(Submitter supplied) Melanocytic nevi are considered to be benign melanocytic proliferations which are driven primarily via BRAF V600E MAPK activation. Using scRNA-seq we explored the signalling pathways in nevus derived melanocytes compared to perilesional skin.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
2 Samples

Download data: MTX, TSV

Series

Accession:: GSE303777

ID:: 200303777

PubMed

Select item 20030060611.

MNX1 prevents somatostatin expression in human beta cells by repressing PERCC1

(Submitter supplied) A highly specific mosaic transcriptional environment guides the fate of pancreatic progenitors during development and next maintains the identity of mature endocrine cells. In mice, one of such transcription factors is MNX1 (motor neuron and pancreas homobox1). It is essential for beta cell development and identity as its deletion in mature beta cells increases their somatostatin expression via an unknown mechanism. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
6 Samples

Download data: TSV

Series

Accession:: GSE300606

ID:: 200300606

Select item 20014032012.

FUNCTIONAL AND TRANSCRIPTOMIC ANALYSIS OF EXTRACELLULAR VESICLES IDENTIFIES CALPROTECTIN AS A NEW PROGNOSTIC MARKER IN PERIPHERAL ARTERIAL DISEASE (PAD)

(Submitter supplied) Rationale: Peripheral arterial disease (PAD) is associated with a high risk of cardiovascular events and death and is postulated to be a critical socioeconomic cost in the future. Extracellular vesicles (EVs) have emerged as potential candidates for new biomarker discovery related to their protein and nucleic acid cargo. Objective: To study prothrombotic activity, cellular origin and transcriptomic profile of circulating EVs and to assess them as prognostic and therapeutic targets in PAD. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
36 Samples

Download data: XLSX

Series

Accession:: GSE140320

ID:: 200140320

SRA Run Selector

Select item 20028091713.

Loss of METTL3 potentiates transposable element expression and drives inflammation-induced cell plasticity in the mammary epithelium [ChIP-seq]

(Submitter supplied) Sustained proliferation and aberrant cellular plasticity are the hallmarks of breast premalignancy, yet the mechanisms driving this process remain unclear. Using CRISPR knockout screens, we systematically characterized the regulators of cellular fitness in the normal mammary epithelium. We found that loss of RNA methyltransferase METTL3 initiates mammary epithelial proliferation and reprograms gene expression, which depends on its catalytic activity. more...

Organism:: Homo sapiens

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

Platform:: GPL18573
6 Samples

Download data: BW

Series

Accession:: GSE280917

ID:: 200280917

Select item 20028091614.

Loss of METTL3 potentiates transposable element expression and drives inflammation-induced cell plasticity in the mammary epithelium [ATAC-seq]

Organism:: Homo sapiens

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

Platform:: GPL18573
6 Samples

Download data: BW

Series

Accession:: GSE280916

ID:: 200280916

Select item 20030745615.

IsomiR Utility in ALS Prognostication [control]

(Submitter supplied) Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive motor neuron loss. IsomiRs are microRNA (miRNA) isoforms that arise from alternative processing or editing events during miRNA biogenesis. While isomiRs may carry distinct biological and clinical relevance, their potential as cell-free biomarkers in neurodegeneration remains largely unexplored. Here we investigated the prognostic utility of plasma isomiRs in ALS, using next-generation sequencing. more...

Organism:: Homo sapiens

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL18573
56 Samples

Download data: XLSX

Series

Accession:: GSE307456

ID:: 200307456

Select item 20029574316.

NF-κB-dependent redistribution of the GR cistrome recruits GR to inflammatory gene loci and correlates with reduced repression by glucocorticoid

(Submitter supplied) While ligand-activated glucocorticoid receptor (GR) binds DNA to activate transcription, glucocorticoids, including budesonide, reduce inflammatory gene expression, yet recruit GR to many such gene loci. In epithelial cells, the inflammatory cytokine, interleukin-1β (IL1B), activates NF-κB to induce gene expression and co-treatment with budesonide produces nanoscale GR-RELA nuclear co-localization. Such co-stimulation orchestrated reciprocal genome-wide redistribution of GR and RELA binding regions (GBRs and RBRs, respectively) relative to each mono-treatment to produce widespread GBR_x0002_RBR overlap. This correlated with increased RNA polymerase-2 presence and required NF-κB for GR cistrome remodeling. Mapping transcription start sites to the nearest GBR or RBR both revealed associations with upregulated, but not repressed, genes. Importantly, RBR proximity to budesonide_x0002_upregulated genes and GBR proximity to IL1B-upregulated genes correlated with attenuated repression on co-treatment. As this occurred on a background of glucocorticoid-induced repression, GR presence at specific IL1B-induced gene loci may reduce, or protect, from an otherwise prevalent glucocorticoid_x0002_induced repression.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
78 Samples

Download data: TXT

Series

Accession:: GSE295743

ID:: 200295743

Select item 20028088117.

Rapid Disease Progression of Myelodysplastic Syndrome is Reflected in Transcriptomic and Functional Abnormalities of Bone Marrow MSCs

(Submitter supplied) Current investigations of MDS-MSCs rely heavily on the clinical international prognostic scoring system (IPSS) or revised IPSS (IPSS-R) of MDS to classify them into either the low- or high-risk categories. This approach, however, suffers from shortcomings, as it is based on assessments of the hematopoietic parameters and may not capture important biological changes or predictors in MDS-MSCs during disease progression. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
22 Samples

Download data: TXT

Series

Accession:: GSE280881

ID:: 200280881

Select item 20027626418.

Comparison of the transcriptome of KP4 controls or resistant to Folfirinox after 96h of treatment with Vehicule or Folfirinox

(Submitter supplied) FOLFIRINOX induces senescence in pancreatic tumor cells. However, some cells can spontaneously escape this senescence. We wanted to characterize the escape mechanisms from FOLFIRINOX-induced senescence of pancreatic tumor cells. Our in vitro adaptation model to FOLFIRINOX shows that cells that have already escaped 5 treatment cycles become less sensitive to FOLFIRINOX.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
4 Samples

Download data: TSV

Series

Accession:: GSE276264

ID:: 200276264

Select item 20021692219.

ChIP-Seq of MYC in MCF-7 cells with EPIC1 knockdown or overexpression.

(Submitter supplied) EPIC1 is reported to interact with MYC through and promote cell-cycle progression. EPIC1 regulate the occupancy of MYC to its target genes.

Organism:: Homo sapiens

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

Platform:: GPL18573
10 Samples

Download data: BW

Series

Accession:: GSE216922

ID:: 200216922

Select item 20030425920.

Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations

(Submitter supplied) Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to study the genomic localization of DNA-associated proteins. However, conventional protocols include multiple manual steps that can introduce inconsistency and limit scalability, thereby restricting the inclusion of appropriate replicates and controls. Although the introduction of liquid handling platforms has improved reproducibility, most existing efforts have automated only a subset of the workflow, and extending automation to efficiently map non-histone proteins, such as chromatin regulators, remains challenging. more...