Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of FACS purified cardiomyocytes from Drosophila melanogaster embryos at stage 13-16.

ABSTRACT: To analyse the transcriptome landscape of differentiating cardiomyocytes, GFP labeled cardiac cells were purified by fluorescent activated cell sorting using the TinC*>GFP transgenic line, and expression profile analysed by deep sequencing.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Charles Girardot

PROVIDER: E-MTAB-4763 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

BiTS Chromatin Immunoprecipitation of H3K4me3 and H3K27ac in Drosophila melanogaster differentiating cardiomyocytes

Project description:Here we improved BiTS-ChIP (Bonn et al, Nature Protocols 7, 978-994 (2012)) to identify active enhancer and promoter elements genome wide in the 104 cardiomyocytes that constitute the Drosophila heart tube and represents only ~0.5% of the total cell content of the embryo. A transgenic Drosophila strain expressing nuclear GFP under the control of a cardiac specific enhancer (TinC*>GFP) was used for staged embryo collections at stages 13-14 (10-13h of development). After embryo fixation and dissociation, intact fixed nuclei were fluorescent labelling. Purification of this rare nuclear population was achieved by a two-step sorting procedure, yielding ~98% purity. Chromatin was extracted and used for immunoprecipitation and sequencing (ChIP-seq) to analyze chromatin modifications at promoters (H3K4me3 and H3K27ac) and enhancers (H3K27ac). Two independent biological replicates (from FACS sorting, chromatin preparations and ChIP-Seq) were performed for each mark and sequenced using Illumina HiSeq.

2017-01-10 | E-MTAB-4584 | biostudies-arrayexpress

ChIP-Seq of six Drosophila species with anti-Drosophila melanogaster Twist and anti-Snail antibodies using different library fragment sizes

Project description:The binding patterns of some transcription factors have been shown to diverge substantially between closely related species. Here, we show that the binding pattern of the developmental transcription factor Twist is highly conserved across six Drosophila species, revealing strong functional constraints at developmental enhancers. Conserved binding correlates with sequence motifs for Twist and its partners, permitting the de novo discovery of their cooperative binding. It also includes over 10,000 low-occupancy sites near the detection limit, which tend to mark enhancers of later developmental stages. We predict that conservation, dynamic occupancy, and combinatorial regulation will be generally true for developmental enhancers.

2010-12-07 | E-MTAB-376 | biostudies-arrayexpress

Single-cell chromatin accessibility profiling of genetically diverse crosses of Drosophila melanogaster during embryogenesis

Project description:Study of context-specific regulation during different developmental time windows of Drosophila melanogaster embryogenesis. Single cell chromatin accessibility was profiled by sciATAC-seq in F1 hybrid embryos obtained by crossing males from four genetically distinct inbred lines from the DGRP collection (Mackay et al. 2012) to females from a common maternal “virginizer” line. F1 embryos were profiled at three key stages of embryonic development: 2-4 hours, 6-8 hours and 10-12 hours after egg laying.

2021-12-21 | E-MTAB-10240 | biostudies-arrayexpress

Whole genome sequencing of a panel of genetically diverse crosses of Drosophila melanogaster

Project description:Whole genome sequencing of 8 F1 Drosophila lines along with the two parental lines for one of the F1 genotypes. Data were sequenced to verify previously published genome sequences (parental lines: DGRP, maternal line: PMID31308546) and to identify potentially unbalanced SNPs within the data that might confound allele-specific measurements in the F1 lines.

2020-12-04 | E-MTAB-8877 | biostudies-arrayexpress

Open chromatin profiling (ATAC-Seq) from genetically diverse crosses of Drosophila melanogaster during embryogenesis

Project description:Open chromatin profiling using Tn5 (ATAC-Seq) for 200,000 nuclei per sample using a panel of 8 F1 hybid D. melanogaster lines. Matched data from the two parental lines of one F1 cross were also collected. All paternal fly lines were taken from the Drosophila Genetic Reference Panel crossed to a common mother (PMID31308546). Data were collected at three time points (2-4h, 6-8h, 10-12h at 25C) with two biological replicates per collection.

2020-12-04 | E-MTAB-8879 | biostudies-arrayexpress

Zfh1 ChIP-seq in Drosophila melanogaster embryos at 4-6h and 6-8h AEL

Project description:Canton S flies (as wild type) were bred at 25C and tightly staged 2-hr embryos were collected after 2 times of 2-hr prelay. The embryos were aged on the apple juice plates and aged to 4-6 and 6-8 hr. For each time point, two independent Chromatin immunoprecipitation (ChIP) experiments were performed using two different antibodies and compared to two independent mock ChIPs using the corresponding pre-immune serum. One Zfh1 antibody was generated in Guinea pig against full-length Zfh1 in the Furlong laboratory, and the other was a generous gift from Dr. Ruth Lehmann. ChIPs were optimized using the enrichment of a binding site identified in a pilot experiment of Zfh1- ChIP-on-chip measured by real-time PCR as previously described. The quality of each IP was also assessed by real-time PCR. Solexa libraries were prepared according to the manufacturer's recommendations. Library quality was assessed on a 2100 Bioanalyzer system (Agilent). All samples were single-end sequenced with 36-bp reads using an Illumina Genome Analyzer IIX by the EMBL Genomics Core Facility.

2019-07-01 | E-MTAB-7422 | 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

Chromatin immunoprecipitation of Biniou protein in Drosophila during embryonic development

Project description:Genomewide mapping of D. melanogaster Biniou protein binding during embryonic development. Four consecutive timepoints (6-8, 8-10, 10-12, 12-14 hrs after egg-laying) were assayed in four independent repeats each. Two different antibodies were used to precipitate the Biniou protein. Additionally the respective preimmune-serum was used as a control for every precipitation. The enriched DNA was hybridized to tiling arrays covering ~ 50% of the Drosophila melanogaster genome.

2007-10-11 | E-TABM-249 | biostudies-arrayexpress

Chromatin immunoprecipitation of Drosophila to identify Biniou protein binding during embryonic development

Project description:Genomewide mapping of D. melanogaster Biniou protein binding during embryonic development. Three consecutive timepoints (6-8, 8-10, 10-12 hrs after egg-laying) were assayed in two independent repeats each. Two different antibodies were used to precipitate the Biniou protein. Additionally the respective preimmune-serum was used as a control for every precipitation. The enriched DNA was hybridized to high density Affymetrix GeneChip Drosophila Tiling 1.0R array.

2009-11-09 | E-TABM-652 | 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