Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Capture-C at paralogous gene loci in Drosophila embryos

ABSTRACT: Capture-C was performed on sonicated and amplified 3C libraries generated from nuclei isolated from fixed 3-18h Drosophila whole embryo samples. Capture-C was performed on wildtype and embryos with deletions or insertions at loop anchors/genes at the respective loci (scyl-chrb or tsh-tio). Capture-C was performed using two different Capture probe pools, one indicated as left (scyl, tsh, salm) and one as right (chrb, tio, salr).

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Drosophila melanogaster

SUBMITTER:

PROVIDER: E-MTAB-13271 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP150044

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Tissue- and stage-specific Capture-C for selected TSS and CRM

Project description:Capture-C was performed on sonicated and amplified 3C libraries generated from nuclei isolated from 2-3h whole embryo samples or Mef2-/Elav-sorted nuclei from 6-8h and 10-12h embryo samples. Capture-C was performed on wildtype embryos. Capture-C was performed using two different Capture probe pools, one for TSS and one for CRM. TSS and CRM were hand curated for tissue- and stage-specific activity.

2023-12-07 | E-MTAB-9310 | biostudies-arrayexpress

Hi-C in D. melanogaster carrying second (CyO) and third (TM3) balancer chromosomes

Project description:We used a Drosophila melanogaster line (a "double balancer") carrying balancer chromosomes for both the second (CyO) and third (TM3) chromosomes, and crossed it to an isogenic wild-type "virginizer" line. Trans-heterozygous adults from the F1 generation were further crossed to the wild-type parental line to obtain the pool of N1 embryos. Allele-specific chromosome conformation capture (Hi-C) was used to measure changes in chromatin organization on both chromosomes.

2019-04-24 | E-MTAB-7512 | biostudies-arrayexpress

Capture-C in D. melanogaster carrying second (CyO) and third (TM3) balancer chromosomes

Project description:We used a Drosophila melanogaster line (a "double balancer") carrying balancer chromosomes for both the second (CyO) and third (TM3) chromosomes, and crossed it to an isogenic wild-type "virginizer" line. Trans-heterozygous adults from the F1 generation were further crossed to the wild-type parental line to obtain the pool of N1 embryos. Allele-specific chromosome conformation capture (Capture-C) was used to measure changes in chromatin organization on both chromosomes.

2019-04-24 | E-MTAB-7513 | biostudies-arrayexpress

Hi-C in the Drosophila wild-type embryos at 2-4h after egg-laying

Project description:Hi-C was performed on 2 biological replicates of wild-type Drosophila embryos at 2-4 hrs after egg-laying. Each library was first checked on MiSeq and then deeply sequenced on HiSeq 2000 (4 lanes for each biological replicate)

2023-05-14 | E-MTAB-12070 | biostudies-arrayexpress

Hi-C in the Drosophila wild-type embryos at 6-8 h and 16-18 hrs after egg-laying

Project description:Hi-C was performed on wild-type Drosophila melanogaster embryos at 6-8 hrs and 16-18 hrs after egg-laying, on 2 biological replicates per time point. Each library was first checked on MiSeq and then deeply sequenced on HiSeq 2000 (4 lanes for each biological replicate). This study completes the E-MTAB-12070 Hi-C dataset on 2-4 hrs wild-type Drosophila melanogaster embryos. Both studies use the same experimental procedures (protocols, sequencer model and run parameters)

2024-01-24 | E-MTAB-13267 | biostudies-arrayexpress

Drosophila melanogaster 4C-Seq experiments in whole embro and mesoderm cells during embryogenesis

Project description:Chromosome conformation capture (4C-Seq) in Drosophila Twist-H2B embryos (carrying nuclear tag specifically in the mesoderm) during embryogenesis was performed, anchoring on 107 different viewpoints. Two timepoints (3-4hrs and 6-8hrs after egg laying) and two tissue context (whole embryo and mesoderm) were assayed. Two independent collections were performed at each timepoint.

2014-06-26 | E-MTAB-2180 | biostudies-arrayexpress

Tissue- and Stage-specific ChIP for H3K27ac, CTCF, Beaf and Su(Hw) in D. melanogaster embryos

Project description:This study contains a series of ChIP-seq experiments performed on nuclear material similar to what was used in Tissue- and Stage-specific Capture-C for selected TSS and CRM (BioStudies/ArrayExpress collection E-MTAB-9310). ChIP-seq with chromatin isolated from nuclei isolated from 2-3h whole embryos samples or Mef2-/Elav-sorted nuclei from 6-8h and 10-12h embryo samples was performed using anti-H3K27ac (Anti-Histone H3 (acetyl K27) antibody, Abcam #ab4729, purified polyclonal), anti-CTCF (rabbit anti Drosophila CTCF antibody, Reinkawitz lab, purified polyclonal), anti-Beaf (mouse anti Drosophila BEAF antibody, DSHB #1553420, monoclonal) and anti-Su(Hw) (goat anti Drosophila Su(Hw) antibody, Geyer lab, purified polyclonal) antibodies.

2023-06-30 | E-MTAB-12639 | biostudies-arrayexpress

Time course DNase assays on Drosophila melanogaster and Drosophila virilis embryos during embryogenesis

Project description:DNase-seq over 3 matching developmental time points in Drosophila melanogaster and Drosophila virilis embryos was performed. The aim is to assess conservation of hypersensitive regions between two distantly related species. Samples were sequenced using Illumina HiSeq.

2019-10-19 | E-MTAB-3797 | biostudies-arrayexpress

Time course DNase assays on Drosophila melanogaster and Drosophila virilis embryos during embryogenesis II

Project description:DNase-seq over 2 matching developmental time points in Drosophila melanogaster and Drosophila virilis embryos was performed. The aim is to assess conservation of hypersensitive regions between two distantly related species. Samples were sequenced using Illumina NextSeq. This Study is an extension to the previously published Study E-MTAB-3797.

2021-05-21 | E-MTAB-9480 | biostudies-arrayexpress

Three-dimensional folding and functional organization principles of the Drosophila genome

Project description:Chromosomes are the physical realization of genetic information and thus form the basis for its reading, hindering and propagation. Here we present a high-resolution chromosomal contact map derived from a new genome-wide chromosome conformation capture approach (a simplified version of the Hi-C method) applied to Drosophila embryonic nuclei. The data show that the entire genome is linearly partitioned into well-demarcated physical domains that overlap extensively with active and repressive epigenetic marks. Chromosomal contacts are hierarchically organized between domains. Global modeling of compaction and clustering of domains show that inactive domains are condensed and confined to their chromosomal territories, while active domains reach out of the territory to form remote intra- and inter-chromosomal contacts. One pilot sample, comprising seven paired-end Illumina GA-II lanes; one deep-sequenced sample, comprising seven paired-end Illumina HiSeq lanes

2012-01-20 | E-GEOD-34453 | biostudies-arrayexpress

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