GPL26167[Accession] - GEO DataSets

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Select item 2002754241.

A Novel Human Protein-Coding Locus Identified Using a Targeted RNA Enrichment Technique

(Submitter supplied) Accurate and comprehensive genomic annotation, including the full list of protein-coding genes, is vital for understanding the molecular mechanisms of human biology. We have previously shown that the genome contains a multitude of yet hidden functional exons and transcripts, some of which might represent novel mRNAs. These results resonate with those from other groups and strongly argue that two decades after the completion of the first draft of the human genome sequence, the current annotation of human genes and transcripts remains far from being complete. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26167
1 Sample

Download data: BED, BEDGRAPH

Series

Accession:: GSE275424

ID:: 200275424

Select item 2002047852.

Full-length direct RNA sequencing uncovers stress-granule dependent RNA decay upon cellular stress

(Submitter supplied) To investigate the role of oxidative stress on RNA dynamics, we treatd HeLa cell lines with 500 µM of arsenite. We then explored the role of XRN1, CHX and ISRIB on mRNA shrotening using the data obtained from dRNA seq

Organism:: Homo sapiens; Mus musculus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL26624 GPL26167 GPL24106
39 Samples

Download data: TAB

Series

Accession:: GSE204785

ID:: 200204785

PubMed

Select item 2002684883.

High-resolution Hi-C reveals increased chromatin looping with senescence associated with hypomethylation and retrotransposon derepression [Long Read DNA-seq]

(Submitter supplied) This study presents the highest-resolution chromatin map of cellular senescence to date, shedding light on how genomic architecture is altered with this damaging phenotype. Senescence, a driver of aging, is a pro-inflammatory state of proliferative arrest caused by DNA damage; it is associated with epigenetic changes, including those to chromatin organization. We created ~3kb Hi-C contact maps of proliferating, quiescent, and replicative senescent lung fibroblasts, and also compared these to oncogene-induced senescence. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL26167
2 Samples

Download data: BED

Series

Accession:: GSE268488

ID:: 200268488

PubMed

Select item 2002658674.

m6ATM: a deep learning framework for demystifying m6A epitranscriptome via Nanopore long read RNA-seq data [HepG2 ]

(Submitter supplied) N6-methyladenosine (m6A) has been one of the most abundant and well-known modifications in mRNA since its discovery in 1970s. Recent studies have demonstrated that m6A gets involved in various biological processes such as alternative splicing and RNA degradation, playing an important role in all kinds of diseases. To better understand the role of m6A, transcriptome-wide m6A profiling data is indispensable. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26167
1 Sample

Download data: BEDGRAPH, TSV

Series

Accession:: GSE265867

ID:: 200265867

Select item 2002561905.

Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing [nanopore]

(Submitter supplied) Quantitative trait loci analyses have revealed an important role for genetic variants in regulating alternative splicing (AS) and alternative cleavage and polyadenylation (APA) in humans. Yet, these studies are generally performed with mature mRNA, so they report on the outcome rather than the processes of RNA maturation and thus may overlook how variants directly modulate pre-mRNA processing. The order in which the many introns of a human gene are removed can substantially influence AS, while nascent RNA polyadenylation can affect RNA stability and decay. more...

Organism:: Homo sapiens

Type:: Other

Platforms:: GPL24106 GPL26167
40 Samples

Download data: TXT

Series

Accession:: GSE256190

ID:: 200256190

Select item 2002702576.

Long-Read Sequencing of an Advanced Cancer Cohort Resolves Rearrangements, Unravels Haplotypes, and Reveals Methylation Landscapes

(Submitter supplied) The Long-read POG dataset comprises a cohort of 189 patient tumours and 41 matched normal samples sequenced using the Oxford Nanopore Technologies PromethION platform. This dataset from the Personalized Oncogenomics (POG) program and the Marathon of Hope Cancer Centres Network includes accompanying DNA and RNA short-read sequence data, analytics, and clinical information. We show the potential of long-read sequencing for resolving complex cancer-related structural variants, viral integrations, and extrachromosomal circular DNA. more...

Organism:: Homo sapiens

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL26167
232 Samples

Download data: TSV

Series

Accession:: GSE270257

ID:: 200270257

PubMed

Select item 2002525347.

ionizing radiation and SRSF1 knockdown in triple-negative breast cancer cells

(Submitter supplied) The goal of this study was to investigate the impact of 10 Gy ionizing radiation (IR) and/or SRSF1 depletion on isoform switching in the triple-negative breast cancer cell line, MDA-MB-231.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26167
12 Samples

Download data: TAR

Series

Accession:: GSE252534

ID:: 200252534

Select item 2002593358.

Targeting the CLK2/SRSF9 splicing axis in prostate cancer leads to decreased ARV7 expression in an rs5918762 allele-dependent manner

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

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL24676 GPL26167
12 Samples

Download data

Series

Accession:: GSE259335

ID:: 200259335

PubMed

Select item 2002593349.

Targeting the CLK2/SRSF9 splicing axis in prostate cancer leads to decreased ARV7 expression in an rs5918762 allele-dependent manner (ONT long read sequencing)

(Submitter supplied) The Cdc2-like kinase (CLK)-family is a regulator of the splicing process. Here, we report the effect of Lorecivivint (SM04690), a CLK/DYRK inhibitor, on alternative splicing in the prostate cancer cell line 22Rv1. Lorecivivint treatment lead to impaired growth and disruption of several oncogenic pathways, including the androgen response, MYC, and Wnt/β-catenin hallmark pathways. Taken together, this data shows that alternative splicing is a pivotal process in prostate cancer and is suitable to be targeted.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26167
6 Samples

Download data: TSV

Series

Accession:: GSE259334

ID:: 200259334

PubMed

Select item 20022376210.

Senescence-associated dysregulation of translation inhibits activation of the integrated stress response

(Submitter supplied) Senescence is a state of indefinite cell cycle arrest associated with aging, cancer, and age-related diseases. Here we find that translational deregulation and a corresponding maladaptive integrated stress response (ISR) is a hallmark of senescence that desensitizes senescent cells to stress. We present evidence that senescent cells maintain high levels of eIF2? phosphorylation, typical of ISR activation, but translationally repress production of the stress response transcription factor 4 (ATF4) by ineffective bypass of the inhibitory upstream open reading frames (uORFs). more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL24106 GPL26167
54 Samples

Download data: TAB, TXT

Series

Accession:: GSE223762

ID:: 200223762

PubMed

Select item 20024979911.

scNanoSeq-CUT&Tag: a long-read single-cell CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells

(Submitter supplied) We developed scNanoSeq-CUT&Tag, a streamlined method by adapting a modified CUT&Tag protocol to Oxford Nanopore sequencing platform for efficient chromatin modification profiling at single-cell resolution. We firstly tested the performance of scNanoSeq-CUT&Tag on six human cell lines: K562, 293T, GM12878, HG002, H9, HFF1 and adult mouse blood cells, it showed that scNanoSeq-CUT&Tag can accurately distinguish different cell types in vitro and in vivo. more...

Organism:: Mus musculus; Homo sapiens

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

Platforms:: GPL26167 GPL26624
46 Samples

Download data: BED, BEDGRAPH, BW, TXT

Series

Accession:: GSE249799

ID:: 200249799

PubMed

Select item 20026341412.

Non-coding cause of congenital heart defects: Abnormal RNA splicing with multiple isoforms as a mechanism for heterotaxy

(Submitter supplied) Heterotaxy is a disorder characterized by severe congenital heart defects (CHDs) and abnormal left-right patterning in other thoracic or abdominal organs. Clinical and research-based genetic testing has previously focused on evaluation of coding variants to identify causes of CHDs, leaving non-coding causes of CHDs largely unknown. Variants in the transcription factor Zinc finger of the cerebellum 3 (ZIC3) cause X-linked heterotaxy. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL26167 GPL24676
17 Samples

Download data: TXT

Series

Accession:: GSE263414

ID:: 200263414

PubMed

Select item 20027563713.

ATF4-Mediated Metabolic Stress Response as a Therapeutic Vulnerability in Chordoma

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

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL26167 GPL21697
50 Samples

Download data

Series

Accession:: GSE275637

ID:: 200275637

Select item 20027563614.

ATF4-Mediated Metabolic Stress Response as a Therapeutic Vulnerability in Chordoma [PDX RNA-seq]

(Submitter supplied) Chordoma, a rare and challenging primary bone malignancy, currently lacks effective targeted therapies. Despite surgical resection and adjuvant radiotherapy, prognosis remains poor. Recent preclinical studies have highlighted potential therapeutic targets, including the transcription factor TBXT, although clinical outcomes have been modest. In this study, we investigated the therapeutic potential of tRNA synthetase inhibitors, specifically halofuginone and halofuginol, in chordoma treatment. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26167
10 Samples

Download data: TSV

Series

Accession:: GSE275636

ID:: 200275636

Select item 20027424915.

Integrative analysis of long isoform sequencing and functional data identifies distinct cortical layer neuronal subtypes derived from human iPSC

(Submitter supplied) Generation of human induced pluripotent stem cells (iPSCs) through reprogramming was a transformational change in the field of regenerative medicine that led to new possibilities for drug discovery and cell replacement therapy. Several protocols have been established to differentiate hiPSCs into neuronal lineages. However, low differentiation efficiency is one of the major drawbacks of these approaches. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26167
4 Samples

Download data: TSV

Series

Accession:: GSE274249

ID:: 200274249

Select item 20023230716.

Nuclear MTHFD2 secures centromere methylation, chromosome stability and correct mitosis progression

(Submitter supplied) Subcellular compartmentalization of metabolic enzymes may elicit specific cellular functions by establishing a unique metabolic environment. Indeed, the nuclear translocation of certain metabolic enzymes is required for epigenetic regulation and gene expression control. Here, we reveal that, in cancer cells, the mitochondrial enzyme methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) localizes in the nucleus during the G2-M phase of the cell cycle to secure mitosis progression. more...

Organism:: Homo sapiens

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL26167
2 Samples

Download data: TXT, VCF

Series

Accession:: GSE232307

ID:: 200232307

Select item 20026312617.

Identification of hypoxia-induced isoforms and novel genes with nanopore long reads sequencing

(Submitter supplied) Long-read nanopore sequencing is capable of continuously reading thousands of base pairs. Here, we report the application of nanopore sequencing technology for analysing hypoxia-specific transcriptomes in normal liver and liver cancer cell lines, which help us to better understand the mechanism of cell survival and metastasis under hypoxia. We conducted transcriptomic sequencing of normal liver and liver cancer cell lines under normoxia or hypoxia, founding that long-read sequencing could detect thousands of hypoxia-specific isoforms and unannotated novel genes. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26167
4 Samples

Download data: TSV

Series

Accession:: GSE263126

ID:: 200263126

Select item 20025043518.

High-density resolution of the Kaposi’s Sarcoma associated Herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing

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

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Other

6 related Platforms
23 Samples

Download data: BEDGRAPH, GTF

Series

Accession:: GSE250435

ID:: 200250435

PubMed Full text in PMC Similar studies

Select item 20025043419.

High-density resolution of the Kaposi’s Sarcoma associated Herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing [iSLK-WTBAC-PCR-cDNA-Seq]

(Submitter supplied) Kaposi’s sarcoma-associated herpesvirus is etiologic agent of Kaposi’s Sarcoma and two B-cell malignancies. Recent advancements in sequencing technologies have led to high resolution transcriptomes for several human herpesviruses that densely encode genes on both strands. However, for KSHV progress remained limited due to overall low percentage of KSHV transcripts even during lytic replication. To address this challenge, we have developed a target enrichment method to increase the KSHV-specific reads for both short- and long-read sequencing platforms. more...