Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [RNA-seq]

ABSTRACT: To investigate the impact of altered transcription and chromatin on steady state transcript levels, we peformed gene expression and splicing analysis in K562 cells (wild type and SF3B1K700E mutant) at 4 and 8 days after mutant allele expression We then performed gene expression profiling analysis using data obtained from RNA-seq at two time points.

ORGANISM(S): Homo sapiens

PROVIDER: GSE226002 | GEO | 2024/03/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [Long read sequencing]

Project description:To understand how SF3B1K700E impacts co-transcriptional splicing, we peformed long read sequencing of RNA (nSRS-seq) in K562 cells (wild type and SF3B1K700E mutant) at 4 days after mutant allele expression We then performed co-transcriptional splicing efficiency analysis using data obtained from Long read sequencing

2024-03-12 | GSE225992 | GEO

Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [nascent RNAseq]

Project description:As a complementary approach to GROseq, we peformed short read sequencing of nascent RNA (nSRS-seq) in K562 cells (wild type and SF3B1K700E mutant) at 4 days after mutant allele expression We then performed nascent gene transcription expression using data obtained from nSRS-seq

2024-03-12 | GSE226000 | GEO

Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [DRIP-seq]

Project description:To investigate the distribution of R-loop formation, we peformed R-loop mapping analysis using S9.6 antibody-based DRIP-seq in K562 cells (wild type and SF3B1K700E mutant) at 4 days after mutant allele expression We then performed metaplot and peak-based analysis using data obtained from DRIP-seq

2024-03-12 | GSE226001 | GEO

Disruption of RNAPII transcription elongation links Oncogenic SFB31 mutations to replciation stress and targetable alterations in chromatin landscape [mNET-Seq]

Project description:To investigate changes in RNAPII distribution in response to SF3B1 mutations, we peformed mNET-seq using antibody against either pan Pol II CTD or Ser2P Pol II CTD in K562 cells (wild type and SF3B1K700E mutant) at 4 days after mutant allele expression We then performed coverage plot analysis using data obtained from mNET-seq to investigate RNAPII distribution changes. Drosophila spike-in was included for the pan-Pol II CTD studies.

2024-03-12 | GSE254793 | GEO

Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [GRO-seq]

Project description:To investigate redistribution of RNAPII in response to the SF3B1 mutation and to study its effects on nascent gene expression, we peformed fastGRO-seq (variant of GRO-seq using 4-thio-UTP based nuclear run-on) in K562 cells (wild type and SF3B1K700E mutant) at 4 days after mutant allele expression We then performed metaplot-based and gene expression analysis using data obtained from fastGRO-seq

2024-03-12 | GSE225999 | GEO

Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [NTD-chIP-seq]

Project description:To investigate changes in RNAPII distribution in response to SF3B1 mutations, we peformed ChIP-seq using antibody against N-terminal domain of RNAPII (Pan-Pol2) in K562 cells (wild type and SF3B1K700E mutant) at 4 days after mutant allele expression We then performed coverage plot analysis using data obtained from ChIP-seq to investigate RNAPII distribution changes

2024-03-12 | GSE225997 | GEO

Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [CDK9-chIP-seq]

Project description:To investigate changes in p-TEFb distribution in response to SF3B1 mutations, we peformed ChIP-seq using antibody against the CDK9 component of pTEFb in K562 cells (wild type and SF3B1K700E mutant) at 4 days after mutant allele expression We then performed coverage plot analysis using data obtained from ChIP-seq from IP and Input fractions to investigate CDK9 distribution changes

2024-03-12 | GSE225996 | GEO

Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [TT-TL seq]

Project description:To investigate how whether the RNAPII defect is premature pause release defect or gene body elongation defect due to splicing factor mutations, we peformed TT-TL-seq (TT seq with a time lapse component) in K562 cells (wild type and SF3B1K700E mutant; U2AF1wild type vs U2AF1 S34F mutant) at 4 days after mutant allele expression We then performed metaplot-based and gene expression analysis using data obtained from TT-TL seq

2024-03-12 | GSE225998 | GEO

Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [Murine ChIP-Seq]

Project description:To investigate changes in Pol2 distribution in response to SF3B1 mutations, we peformed ChIP-seq using antibody against Pol2 (both CTD and elongation specific (Ser2P and Ser5p). For the murine model, SF3B1 mutant (and WT counterparts) were treated with tamoxifen daily x 5 days at 5 weeks of age. Mice were euthanized at end of week 7 and bone marrow was harvested to isolate lineage negative cells We then performed coverage plot analysis using data obtained from ChIP-seq from IP fractions to investigate Pol2 distribution changes

2024-03-12 | GSE254792 | GEO

Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [NTD-Seq]

Project description:To investigate changes in RNAPII distribution in response to SF3B1 mutations, we peformed ChIP-seq using antibody against N-terminal domain of RNAPII (Pan-Pol2) in K562 cells We then performed coverage plot analysis using data obtained from ChIP-seq to investigate RNAPII distribution changes

2024-03-12 | GSE254796 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data