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Genomic annotation of a non-coding region deleted on 4q25 [CUT&RUN]

ABSTRACT: Genomic annotation of a non-coding region deleted on 4q25 [CUT&RUN]

PROVIDER: PRJNA1020428 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR26156326_1.fastq.gz	Fastqsanger.gz
	SRR26156326_2.fastq.gz	Fastqsanger.gz
	SRR26156327_1.fastq.gz	Fastqsanger.gz
	SRR26156327_2.fastq.gz	Fastqsanger.gz
	SRR26156328_1.fastq.gz	Fastqsanger.gz

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Genomic annotation of a non-coding region deleted on 4q25

Project description:Genomic annotation of a non-coding region deleted on 4q25

| PRJNA1020425 | ENA

Genomic annotation of a non-coding region deleted on 4q25 [ATAC-seq]

Project description:Genomic annotation of a non-coding region deleted on 4q25 [ATAC-seq]

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Genomic annotation of a non-coding region deleted on 4q25 [CUT&RUN]

Project description:we identified 7 families presenting a new cardiac entity associated with a heterozygous deletion of 2 CTCF binding sites on 4q25, inducing TAD fusion and chromatin conformation remodeling. The CTCF binding sites are located in a gene desert at 1 Mb from the Paired-like homeodomain transcription factor 2 gene (PITX2).

2023-09-28 | GSE243901 | GEO

Genomic annotation of a non-coding region deleted on 4q25

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

2023-09-28 | GSE243902 | GEO

Genomic annotation of a non-coding region deleted on 4q25 [ATAC-seq]

2023-09-28 | GSE243900 | GEO

Cattle Cleavage Under Targets & Release Using Nuclease (CUT&RUN) for CENP-A locus identification

Project description:CUT&RUN experiment was carried out on bovine semeimbranosous muscle satellite cells to identify the locus of the accumulation of the centromeric protein A (CENP-A) on the cattle Y-chromosome. This was carried out to support the annotation of the DNA signal comprising tandem array of a centromeric satellite signal which characterizes the centromere on the Y-chromosome.

2024-10-02 | GSE262830 | GEO

INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA

Project description:This SuperSeries is composed of the following subset Series: GSE35082: INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (expression) GSE35329: INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (SNP data) GSE35367: INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (CGH) Refer to individual Series

2012-07-31 | E-GEOD-35383 | biostudies-arrayexpress

Bulk Cut&run and Cut&tag

Project description:Bulk Cut&run and Cut&tag

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Dynamic dysregulation of the transcriptome upon deletion of Mecp2 in adult mice [CUT&RUN]

Project description:Loss of function mutations in methyl Cpg binding protein 2 (MECP2) cause Rett syndrome. Loss of MeCP2 causes global transcriptional dysregulation, but it was unknown whether this transcriptional dysregulation was proximal to Mecp2 function. We deleted Mecp2 from adult mice and performed a time-series CUT&RUN experiment to identify if MeCP2 binding or histone post-translational modficiations are altered immediately upon loss of MeCP2.

2024-12-16 | GSE246664 | GEO

Demonstration of CUT&RUN motif footprint analysis using key blood progenitor transcription factors

Project description:We introduce CUT&RUNTools (https://bitbucket.org/qzhudfci/cutruntools/) as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&RUN primary cleavage data. CUT&RUNTools extracts endonuclease cut site information from sequences of short read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CUT&RUN. We illustrate the functionality of CUT&RUNTools through analysis of CUT&RUN data acquired for GATA1, a master regulator in erythroid lineage cells. Results were compared initially to published GATA1 ChIP-seq data for cells under the same conditions. We performed de novo analysis of CUT&RUN peaks to retrieve not only GATA1’s primary motif, but also the GATA1-TAL1 composite motif, and co-factor motifs GCCCCGCCTC, CMCDCCC, and RTGASTCA that correspond to SP1, KLF1, and NFE2 co-factors. Cofactor binding was verified by independent TAL1 and KLF1 CUT&RUN, and other ChIP-seq experiments. CUT&RUNTools also generated base-pair resolution motif footprint for sequence-specific binding factors, and located likely direct binding sites by quantifying log-odds of binding scores. Overall, CUT&RUNTools should enable biologists to realize advantages of cleavage data provided by CUT&RUN, and make high-quality footprinting analysis accessible to a broad audience.

2019-08-24 | GSE136251 | GEO

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