Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq of RAD50∆5.1 null mutant and WT W1118 larval stage 3 CNS

ABSTRACT: This experiments follows up ChIPseq experiments and aims to investigate the role of Rad50 on gene expression in drosophila larval stage 3 CNS.

INSTRUMENT(S): NextSeq 2000

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Thomas Boutet

PROVIDER: E-MTAB-13490 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome analysis of wandering larval hemocytes in Toll10b and gcm background in Drosophila

Project description:The aim of the experiment is to establish the impact of the interaction between the hemocyte differentiation factor gcm and the Toll pathway in the immune cells of the Drosophila larva. The hemocytes were collected from 3rd instar larvae of the following genotypes: Toll10B/+, gcm26/+ and gcm26/+;Toll10B/+.

2023-06-09 | E-MTAB-11970 | biostudies-arrayexpress

Genome-wide transcriptomic effects of the foraging gene shed light on genetic pathways that regulate pleiotropy and plasticity

Project description:Natural variants of the Drosophila melanogaster foraging (for) gene as a popular model to understand behaviour, plasticity, and pleiotropy at an evolutionary and molecular level. The effects for variants on phenotype, fitness, stimulus-response (e.g., food deprivation), and tissue-specific for expression are well characterized. In contrast, the transcriptome-wide influence that for variants have across different tissues and stimuli remains unknown. In this study, we collected fed and 4-hour food-deprived D. melanogaster samples from the genetic null, the natural sitter variant, and the natural rover variant in the CNS (brain and brain stem), gut, and fat (89 samples total, N=4-5 per condition/genotype/tissue). Paired-end bulk RNA sequencing was then completed in one experimental batch at Genome Quebec using the NovaSeq6000 S4 PE100 Sequencing Lane. Briefly, samples were aligned to the dm6 genome using STAR, duplicates were marked with Picard, and reads that were non-chromosomal, low-quality, or unpaired were filtered with samtools. High-quality reads were then counted to the dm6 genome with the "Drosophila_melanogaster.BDGP6.22.96" genome annotation with featurecounts. These RNA-seq data elucidated how the for locus, and the natural variants of for can influence gene expression and cellular function across tissues and conditions.

2023-03-15 | E-MTAB-12688 | biostudies-arrayexpress

ChIP-seq of H3K4me3 and H3K27me3 histone marks in the hypothalamus of 35 days-old control and thermally-manipulated chickens

Project description:The experiment aimed at investigating the profiles of two histone marks (H3K27me3 and H3K4me3) in hypothalamus tissues of 35 days-old control (n=3) and thermally-manipulated (cyclic rise in egg incubation temperature of 1.5°C from days 7 to 16 of embryogenesis; n=3) chickens.

2019-10-31 | E-MTAB-7300 | biostudies-arrayexpress

ATAC-seq on sorted neurons from staged E16 or L3 neurons

Project description:Investigate differences in chromatin accessibility during development in E16 and L3 neurons

2023-12-01 | E-MTAB-13491 | biostudies-arrayexpress

ChIP-seq of H3K4me3 and H3K27me3 histone marks in Pectoralis major muscle of 35 days-old control and thermally-manipulated chickens

Project description:The experiment aimed at investigating the profiles of two histone marks (H3K27me3 and H3K4me3) in muscle tissues (Pectoralis major) of 35 days-old control (n=3) and thermally-manipulated (cyclic rise in egg incubation temperature of 1.5°C from days 7 to 16 of embryogenesis; n=3) chickens.

2019-10-31 | E-MTAB-7297 | biostudies-arrayexpress

RNA-seq comparing transcriptome of lymphoblastic cells from FAME patients and control individuals

Project description:RNAseq was performed for 10 individuals: three affected individuals (CSDN4, CSDN5, CSDN6) and one healthy spouse (CSDN7) from Family 1, three affected individuals (CSDN1, CSDN2, CSDN3) from Family 5 and three healthy controls (CSDN8, CSDN9, CSDN10).

2019-09-16 | E-MTAB-8301 | biostudies-arrayexpress

RNAseq of young adult C. elegans animals fed on three different bacterial diets, E. coli OP50, B. subtilis PXN21 and a mixture of both

Project description:To uncover the host response pathways that are modified by a B. subtilis diet and that may provide the protective effect against α-synuclein aggregation, we performed comparative global transcriptomics analysis using next generation RNA sequencing (RNA-seq). We compared young adult animals fed on three different diets, E. coli OP50 and B. subtilis PXN21 lawns, consisting of both spores and vegetative cells, and a mixture of both bacteria.

2020-01-14 | E-MTAB-8164 | biostudies-arrayexpress

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs (4C-Seq)

Project description:During limb development, Hoxd genes are transcribed in two waves: Early on, when the arm and forearm are specified and subsequently, when digits form. While the latter phase is controlled by enhancers centromeric to the HoxD cluster, we show here that the early phase requires enhancers located in the opposite telomeric gene desert. The transition between the two types of regulations involves a functional switch between two distinct topological domains, as reflected by a subset of genes mapping centrally into the cluster, which initially interact with the telomeric domain and subsequently shift to establish new contacts on the opposite side. This transition between two regulatory landscapes generates an intermediate area of low Hox dose developing into the wrist, the transition between our arms and our hands. This intriguing correspondence between genomic and morphological boundaries illustrates the mechanism underlying collinear Hox gene regulation in our developing appendages. Circular Chromosome Conformation Capture (4C seq) at the HoxD locus in developing proximal and distal limbs at E9.5 and E12.5

2013-06-07 | E-GEOD-45455 | biostudies-arrayexpress

Genome-wide maps of m6dA bases in drosophila ovary genomic DNA

Project description:We report the m6dA modification on the Drosophila genome. We collected ovary genomic DNA from 2-day wild-type and DMAD mutant files and performed DNA-immunoprecipitation(DNA-IP)experiments using anti-m6dA antibody. The generated DNA library was subjected to a high-throughput deep sequencing analysis. In this assay, the IgG-immunoprecipited DNA from the same amount of wild-type ovaries was used as the control, and the high-throughput sequencing resulted in a range of approximately 3 to 4.6 million reads. In sum, we identified 50 and 195 peaks from wild-type and DMAD mutant samples. Importantly, m6dA is mainly utilized to modify the transposon sequence on the chromosomes. Examination of m6dA modifications in Genomic DNA of WT and DMAD mutant ovary.

2016-06-01 | E-GEOD-64340 | biostudies-arrayexpress

SOX2 overexpression effect on human lung squamous cells

Project description:We have identified SOX2 as a new oncogene and a likely driver of recurrent 3q26.3 amplifications in lung Squamous Cell Carcinoma. SOX2 is a crucial transcription factor implicated in Embryonic and Neural Stem Cells, that we found widely activatd in human lung SCC. This part of the study aimed at analyzing the transcriptomic consequences of SOX2 overexpression in a simple in vitro model (human lung squamous immortalized cells). Human lung squamous BEAS-2B cells were transduced for Control or SOX2 expression, and their transcriptomes compared using Affymetrix arrays.

2010-02-21 | E-GEOD-14883 | 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