Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional networks controlling the cell cycle

ABSTRACT: In this work, we use RNAi and subsequent RNA isolation and Affymetrix Expression array analysis to map the genome-wide transcriptional targets of 107 of the strongest cell cycle regulators. Drosophila S2 cells were used with RNAi target gene knockdown compared to control (GFP dsRNA). RMA normalized data re-annotated using a custom CDF is available on the FTP site for this experiment. E-MTAB-1648, E-MTAB-1364 and E-MTAB-453 are all data from: Bonke M, et al. (2013) Transcriptional networks controlling the cell cycle. G3 (Bethesda) 3, 75-90, PMID: 23316440.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Jussi Taipale

PROVIDER: E-MTAB-453 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Transcriptional networks controlling the cell cycle.

Bonke Martin M Turunen Mikko M Sokolova Maria M Vähärautio Anna A Kivioja Teemu T Taipale Minna M Björklund Mikael M Taipale Jussi J

G3 (Bethesda, Md.) 20130101 1

In this work, we map the transcriptional targets of 107 previously identified Drosophila genes whose loss caused the strongest cell-cycle phenotypes in a genome-wide RNA interference screen and mine the resulting data computationally. Besides confirming existing knowledge, the analysis revealed several regulatory systems, among which were two highly-specific and interconnected feedback circuits, one between the ribosome and the proteasome that controls overall protein homeostasis, and the other ...[more]

PMID: 23316440

Similar Datasets

Expression data from vegetative tissues of grain, sweet and bioenergy sorghums

Project description:We developed a commercially available whole-transcriptome sorghum microarray (Sorgh-WTa520972F) and generated this dataset to identify tissue and genotype-specific expression patterns for all identified Sorghum bicolor exons and UTRs. The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast and mitochondrial genomes. Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e.g., microRNAs), and confirmed functional small RNAs in related species (corn and sugarcane) were also included in our array design. 78 samples were analyzed from four different tissue types (shoot, seedling, leaves and stem), two dissected stem tissues (pith and rind) and six diverse genotypes (PI455230, Atlas, PI152611, AR2400, R159, and Fremont)

2013-12-31 | E-GEOD-49879 | biostudies-arrayexpress

Congenic dissection of a major QTL for methamphetamine sensitivity implicates epistasis

Project description:We identified a congenic mouse with an introgressed region from the A/J donor inbred strain on an inbred C57BL/6J background that showed a reduced locomotor stimulant response to methamphetamine. We conducted microarray analysis of the striatum from drug-naive female and male mice that were 6-9 weeks old. The congenic region is on chromosome 11 and spans approximately 84-96 Mb. There were two groups of mice used in the analysis: B6 control mice versus congenic mice. Congenic mice were collapsed across heterozygous and homozygous genotypes. All mice are on a C57BL/6J background. Congenic mice differ only on chromosome 11 where they contain the introgressed A/J alleles from 84-96 Mb. 14 C57BL/6J wildtype mice and 14 B6.A/J congenic mice (84-96 Mb region from A/J strain) were examined for gene expression differences using striatal tissue (left and right punches pooled). All mice were drug-naïve and were 6-9 weeks old at the time of sacrifice.

2012-01-18 | E-GEOD-35139 | biostudies-arrayexpress

Transcriptional networks controlling the cell cycle (RNA-seq)

Project description:Transcription profiling by RNA-seq of Drosophila S2 cells after knock down of strongest cell cycle regulators to map their genome-wide transcriptional targets (155 assays). RNA samples used for this experiment are a subset of the 200 samples used in Affymetrix microarray experiment E-MTAB-453. E-MTAB-1648, E-MTAB-1364 and E-MTAB-453 are all data from: Bonke M, et al. (2013) Transcriptional networks controlling the cell cycle. G3 (Bethesda) 3, 75-90, PMID: 23316440.

2012-11-26 | E-MTAB-1364 | biostudies-arrayexpress

Re-analysis of E-MTAB-1585

Project description:Raw data from E-MTAB-1585 was normalized by using reads per million. https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585/

2013-09-19 | GSE50860 | GEO

Imprinting RNAseq

Project description:Long-term hematopoietic stem cells (HSCs), short-term HSCs and multipotent progenitor cells (MPPs) were isolated from bone marrow of four mouse strains (WT, H19-deletion, Igf1r-deletion, and double-deletion) and expression profiled with RNAseq. The behavior of the transcriptomes, and in particular the imprinted genes, was analyzed to see what might be involved in maintaining quiescence of long-term stem cells, and how H19 and Igf1r affected the expression of imprinted genes. Transcriptional profiling data of the same cells have been deposited in ArrayExpress under accession number E-MTAB-1644 (http://wwwdev.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1644/).

2013-08-12 | E-MTAB-1628 | biostudies-arrayexpress

Transcriptome analysis of peripheral blood monocytes

Project description:RNA sequencing data of peripheral blood monocytes to assess their transcriptomic differences, in particular metabolics, compared to ascites fluid-derived tumor associated macrophages (datasets publicly available; E-MTAB-3167 and E-MTAB-4162)

2019-10-01 | GSE89187 | GEO

Effects of purine de novo synthesis knockdown on gene expression in Drosophila melanogaster S2 tissue culture cells

Project description:The effect of inhibiting expression of the ade2 gene by RNA interference in Drosophila S2 tissue culture cells was examined. S2 cells underwnt three different dsRNA treatments. Two were for non-overlapping sequences of ade2 transcripts and the third was for a non-specific Chlamydomonas reinhardtii lhcb sequence. 3 samples from ade2 dsRNA-1 treated cells, 2 samples from ade2 dsRNA-2, and 3 samples from lhcb dsRNA treated cells were used on two 4x44K format slides (G2519F).

2010-12-01 | E-GEOD-24123 | biostudies-arrayexpress

Methylation profiling by array of human and TC1 and TC0 mouse strain livers and testes to study human repetitive elements on human chromosome 21 in a heterologous mouse environment

Project description:The aim of this project is to study human repetitive elements on human chromosome 21 in a heterologous mouse environment (Tc1 mouse). To determine the unbiased regulation of the human genome, suppressed regions of human chromosome 21 were identified in vivo in liver and testes of human and Tc1 mouse by Illumina Infinium HumanMethylation450k beadrray. The complementary dataset characterising activated chromosomal regions (H3K4me3) and transcription factor binding sites profiled by ChIP-seq is available under accession E-MTAB-1104.

2012-12-13 | E-MTAB-1304 | biostudies-arrayexpress

RNA-seq of human whole-blood samples before and after the administration of recombinant human erythropoietin

Project description:As part of cross-platform comparisons of microarray and RNA-seq, the current experiment using the Illumina NextSeq 500 and MGI DNBSEQ-G400RS aimed to quantify gene-level expression in subjects administered recombinant human erythropoietin over a 10-week protocol for the identification of gene signatures of blood doping. These results were compared to results obtained from other gene expression quantification platforms using the same experimental cohort, including the Illumina HumanHT-12v4 Expression BeadChips (archived in ArrayExpress; E-MTAB-2874) and Affymetrix Human Transcriptome Array 2.0 (archived in ArrayExpress; E-MTAB-11080).

2021-11-04 | GSE186294 | GEO

Analysis of cardiac miRNA expression in the early neonatal period

Project description:The regenerative capacity of the mammalian heart is lost quickly after birth when cardiomyocytes stop dividing and undergo cell cycle arrest. Thus, the adult mammalian heart lacks the ability to heal itself to any appreciable amount after ischemic injury such as myocardial infarction. Heart growth begins during fetal life with the first phase of DNA synthesis that is exclusively associated with cardiomyocyte proliferation. This process proceeds until 12 hours after birth and is defined as 0 days in our submitted samples. Cardiomyocytes division is undetectable at neonatal day 1. To analyze the molecular mechanisms responsible for cessation of cardiomyocyte proliferation, we performed genome-wide miRNA microarray profiling by comparing postnatal days 0 vs 1d.This revealed a profile of 8 significantly downregulated miRNAs in the proliferative DKO hearts (versus vehicle-injected control), that were enriched for mRNA targets involved in cell cycle regulation. In vitro studies have demonstrated that knockdown of these 8 miRNAs in neonatal rat cardiomyocytes can increase the occurrence of cytokinetic events. Ultimately, we aim to inject antagomirs targeting these miRNAs into mice post-myocardial infarction to determine the effect of these miRNAs on heart function and cardiomyocyte proliferation in vivo.

2022-01-30 | E-MTAB-9256 | 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