Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Poly(A) mRNA-seq of Drosophila embryos at NC14 depleted of Beaf-32, CTCF or CP190

ABSTRACT: Profiling of genes expression changes caused by the depletion of either Beaf-32, CP190 or CTCF during early embryogenesis. Gene expression changes were profiled in embryos at NC14 (manually-selected). Beaf-32 and CP190 were depleted using RNAi and CTCF by using maternal/zygotic null embryos. Poly(A) mRNA-seq was performed from three biological replicates.

INSTRUMENT(S): NextSeq500

ORGANISM(S): Drosophila melanogaster

SUBMITTER:

PROVIDER: E-MTAB-11978 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP139559

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Hi-C in Drosophila embryos at NC14 depleted of Beaf-32, CP190 or CTCF using the Bridge Adaptor Protocol

Project description:Hi-C was performed using the Bridge Adaptor Protocol in 2 biological replicates of Drosophila embryos at NC14 depleted of the maternal deposition of Beaf-32, CP190 or CTCF mRNA and protein. Embryos were collected at 2-3h AEL and were derived from mothers expressing RNAi against Beaf-32 or CP190 in the germline, or were genetic null for the maternal and zygotic contribution of CTCF.

2022-12-17 | E-MTAB-9158 | biostudies-arrayexpress

Chromatin immunoprecipitation of Drosophila embryos at NC14 to identify binding sites of Beaf-32, CP190, CTCF, Su(Hw) and GAF insulator proteins

Project description:ChIP-seq against Beaf-32, CP190, CTCF, Su(Hw) and GAF was performed in wild-type embryos collected between 2h10 and 2h40 after egg laying (corresponding to the stage NC14). For each protein, ChIP-seq was done in biological duplicates. Matched input controls were also generated. Sequencing was performed on Illumina NextSeq 500.

2022-12-17 | E-MTAB-9156 | biostudies-arrayexpress

CUTnTag against Beaf-32, CP190 and CTCF in Drosophila melanogaster wild-type and insulator-depleted embryos at stage NC14

Project description:CUTnTag against Beaf-32, CP190 and CTCF was performed in wild-type and insulator-depleted embryos collected between 2h10 and 2h40 after egg laying (corresponding to the stage NC14). Spike-ins from D. virilis were used in each reaction. For each sample, 50k nuclei from each species were mixed together at the start of the protocol. For each protein, CUTnTag was done in biological duplicates. Sequencing was performed on Illumina NextSeq 500.

2022-12-17 | E-MTAB-11993 | biostudies-arrayexpress

Chromatin immunoprecipitation of Drosophila embryos at 6-8h AEL to identify Beaf-32, CP190, CTCF and SuHw proteins binding

Project description:ChIP-seq against Beaf-32, CP190 or CTCF was performed in wild-type embryos collected between 6 and 8h after egg laying. For each protein, ChIP-seq was done in biological duplicates. Matched input controls were also generated.

2023-10-31 | E-MTAB-9157 | biostudies-arrayexpress

Chromatin immunoprecipitation of Drosophila embryos at NC14 to identify Beaf-32, CP190 and CTCF proteins binding

Project description:Chromatin immunoprecipitation of Drosophila embryos at NC14 to identify Beaf-32, CP190 and CTCF proteins binding

| PRJEB38466 | ENA

Poly(A) mRNA-seq of Drosophila embryos at NC14 depleted of Beaf-32, CTCF or CP190

Project description:Poly(A) mRNA-seq of Drosophila embryos at NC14 depleted of Beaf-32, CTCF or CP190

| PRJEB54710 | ENA

CUTnTag against Beaf-32, CP190 and CTCF in Drosophila melanogaster wild-type and insulator-depleted embryos at stage NC14

Project description:CUTnTag against Beaf-32, CP190 and CTCF in Drosophila melanogaster wild-type and insulator-depleted embryos at stage NC14

| PRJEB54783 | ENA

Hi-C in Drosophila embryos at NC14 depleted of Beaf-32, CP190 or CTCF using the Bridge Adaptor Protocol

Project description:Hi-C in Drosophila embryos at NC14 depleted of Beaf-32, CP190 or CTCF using the Bridge Adaptor Protocol

| PRJEB38468 | ENA

Genome-wide binding profiles of Drosophila melanogaster insulator proteins in Kc and Mbn2 cells

Project description:ChIP-chip experiments with NimbleGen whole-genome tiling arrays to compare Su(Hw), dCTCF, BEAF, and CP190 localization on DNA in Kc and Mbn2 cells revealed that BEAF is a third subclass of CP190-containing insulators. The DNA binding proteins, Su(Hw), dCTCF, and BEAF show unique distribution patterns with respect to the location and expression level of genes, suggesting diverse roles for these three subclasses of insulators in genome organization. Notably, cell line specific localization sites for all three DNA binding proteins as well as CP190 indicate multiple levels at which insulators can be regulated to affect gene expression.

2009-05-15 | GSE15661 | GEO

Essential role of Cp190 in physical and regulatory boundary formation in Drosophila

Project description:Animal genomes fold into contact domains defined by enhanced internal contact frequencies with debated functions in establishing independent gene regulatory domains. A large fraction of contact domains in mammals are formed by stalling of chromosomal loop-extruding cohesin by CTCF at domain boundaries. 90% of domain boundaries in Drosophila form CTCF-independently, and other proteins were proposed to form chromosomal loops with dual functions of segregating promoters from inappropriate regulatory elements and connecting distal regulatory elements to their correct targets. Here, we genetically ablate the ubiquitous boundary-associated factor Cp190 and assess impacts on genome folding and transcriptional regulation in embryos. Our results reveal that Cp190 is a major factor required for contact domain boundary formation and gene insulation in Drosophila.

2022-05-30 | PXD027795 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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