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

ABSTRACT: 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

ORGANISM(S): Homo sapiens

PROVIDER: GSE226001 | GEO | 2024/03/12

REPOSITORIES: GEO

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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 [RNA-seq]

Project description: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.

2024-03-12 | GSE226002 | 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 [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 [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

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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 [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

Genome-wide strand-specific R-loops mapping in E. coli DY330 using DRIP-Seq

Project description:Distribution of R-loops on genomic sites was studied for exponentially growing Escherichia coli in different conditions using strand-specific DRIP-Seq with S9.6 antibodies.

2022-01-01 | GSE181945 | GEO

Human and mouse DRIP-seq and DRIPc-seq

Project description:This study profiles RNA:DNA hybrid formation in human and mouse cell lines. DRIPc-seq (strand-specific R-loop mapping) was performed on human NT2 cells and mouse 3T3 cells. DRIP-seq (R-loop mapping) was performed on human NT2 and K562 and mouse E14 and 3T3 cell lines. MethylC-seq and RNA-seq were performed on NT2.

2016-06-30 | E-GEOD-70189 | biostudies-arrayexpress

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