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The BAF complex does not mediate GLI repression (RNA-Seq)

ABSTRACT: The BAF complex does not mediate GLI repression (RNA-Seq)

PROVIDER: PRJNA934434 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23336492.fastq.gz	Fastqsanger.gz
	SRR23336493.fastq.gz	Fastqsanger.gz
	SRR23336494.fastq.gz	Fastqsanger.gz
	SRR23336495.fastq.gz	Fastqsanger.gz

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The BAF complex does not mediate GLI repression

Project description:The BAF complex does not mediate GLI repression

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The BAF complex does not mediate GLI repression (ATAC-Seq)

Project description:The BAF complex does not mediate GLI repression (ATAC-Seq)

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The BAF complex does not mediate GLI repression (WT Cut&RUN)

Project description:The BAF complex does not mediate GLI repression (WT Cut&RUN)

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The BAF complex does not mediate GLI repression (Gli3 null Cut&RUN)

Project description:The BAF complex does not mediate GLI repression (Gli3 null Cut&RUN)

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The BAF complex does not mediate GLI repression (ATAC-Seq)

Project description:Purpose: This study seeks to determine whether Smarcc1 mediates GLI repression through chromatin compaction in the limb. Methods: To determine if Smarcc1 mediated GLI repression through chormatin compaction, we used genomic approached to determine changes in chromatin accessibility in control and Smarcc1-conditional mutants. We performed ATAC-seq on individually genotyped anterior forelimbs at E11.5 (40-48s) on control (2 replicates) and PrxCre/+;Smarcc1c/c (3 replicates) embryos. From this experiment we identified ~10,000 differentially accessible regions (FDR<0.05). Results: We find that SMARCC1 is required to maintain chromatin accessibility at thousands of regions within the mouse limb, including most HH-responsive GLI enhancers

2024-02-03 | GSE224506 | GEO

The BAF complex does not mediate GLI repression (WT Cut&RUN)

Project description:Purpose: This study seeks to identify SMARCC1-bound regions in the mouse limb. Methods: To identify SMARCC1 bound regions in the limb, we performed Cut&Run on pooled anterior and posterior wild-type forelimbs at E11.5 (43-44s; 3 replicates each) and on whole forelimb pairs at E9.5 (21-24s; 2 replicates). We identified 28,082 SMARCC1-bound regions in the anterior forelimb at E11.5, 42,530 regions in the E11.5 posterior limb, and 10,792 SMARCC1-bound regions at E9.5 (FDR<0.05). Results: We find that SMARCC1 is bound to most limb enhancer regions at late stages (E11.5). Additionally, We find that SMARCC1 is bound to the majority of HH-responsive GLI enhancers at E11.5 but only a small portion of GLI enhancers at E9.5.

2024-02-03 | GSE224507 | GEO

The BAF complex does not mediate GLI repression (Gli3 null Cut&RUN)

Project description:Purpose: This study seeks to determine whether GLI3 is required to recruit the SMARCC1 complex to GLI enhancers in the limb. Methods: To determine if Gli3 is required to recruit SMARCC1 to its anhancers, we performed differential chromatin binding to compare SMARCC1 binding in control and Gli3 mutants. We performed Cut&Run for SMARCC1 binding on individually genotyped E11.5 (40-43s) anterior forelimb pairs from control (Gli3+/+; 3 replicates) and Gli3 mutant (Gli3-/-; 4 replicates) embryos. Results: We found that there is no major difference in SMARCC1 binding in Gli3-mutants compared to controls.

2024-02-03 | GSE224508 | GEO

The BAF complex does not mediate GLI repression

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-02-03 | GSE224510 | GEO

The BAF complex does not mediate GLI repression (RNA-Seq)

Project description:Purpose: This study seeks to determine whether Smarcc1 co-regulates Hedgehog (HH) target genes in the limb. Methods: To determine if Smarcc1 is required to regulate HH targets, we used genomic approaches to identify Smarcc1-regulated genes within the forelimb. We performed bulk RNA-seq on individually genotyped forelimb-bud pairs at E11.5 (39-40s) on control (2 replicates) and PrxCre/+;Smarcc1c/c (2 replicates) embryos. From this experiment we identified 928 differentially expressed genes (FDR<0.05). Results: We find that while certain HH target genes are co-regulated by SMARCC1, the majority of HH target genes do not require Smarcc1.

2024-02-03 | GSE224505 | GEO

GLI transcriptional repression is inert prior to HH pathway activation

Project description:Purpose: Most Hedgehog responsive gene expression is mediated through GLI de-repression. Additionally GLI -repression is proposed to play roles in limb pre-patterning before HH pathway activation. This study evaluates if GLI repression is established prior to HH pathway activation. Methods: To determine if GLI-repression is established prior to pathway activation, we used genomic approaches to study GLI-mediated repression using the mouse developing limb as a model. We identified pre-HH (E9.25, 21-23S) and post-HH (E10.5, 32-25S) GLI3 binding regions using CUT&RUN for endogenous FLAG-tagged GLI3 proteins. Using a combination of ChIP-seq, CUT&RUN, CUT&Tag, ATAC-seq and RNA-seq, we tested whether loss of Gli3 prior to HH signaling was able to de-repress genes and enhancers, as it does after HH signaling. Results: Prior to HH signaling, GLI3 binds to poised, accessible regions with histone deacetylase (HDAC) proteins, similar to post-HH signaling. Despite GLI3 binding to most regions as it does in the post-HH limb, loss of Gli3 is unable to prematurely active target genes or enhancers. Furthermore, we find that GLI3-dependent chromatin compaction does not occur until roughly 10 hours after HH signaling would have normally been induced. Collectively, these results support that GLI repressor proteins are inert prior to HH pathway activation.

2022-01-21 | GSE178838 | GEO

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