Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic profile of children with septic shock with versus without immunoparalysis

ABSTRACT: Critically ill children with septic shock enrolled in prospective observational study. Children were divided into two groups based on the presence or absence of immunoparalysis (defined by ex vivo LPS-induced TNF alpha response). Total RNA isolated and sequenced by RNAseq and differential expression analyses performed.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Jennifer Muszynski

PROVIDER: E-MTAB-10938 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Cisplatin induces the rearrangement of RBPs on CDKN1B/p27 mRNA

Project description:Cisplatin (CP) is a chemotherapeutic drug that is used to cure different types of cancer. CP induces DNA damage and leads to cell cycle arrest. The cyclin-dependent kinase inhibitor 1B (CDKN1B), also termed p27, plays an important role in the drug response ; and increased levels of p27 correlated with CP resistance. In HEK293 cells, we observed that p27 mRNAs levels increased whereas protein level drastically decreased in cells treated with CP; suggesting post-transcriptional regulatory events. To further understand the underlying mechanisms, we applied a biochemical approach combined with mass-spectrometry to systematically identify the RNA-binding proteins (RBPs) that are bound to the 3’UTR of p27 mRNAs in CP-treated versus non-treated cells in vivo. We found that 24 proteins, most of them known RBPs such HuR, hNRNPD, changed their association with p27 mRNA upon CP treatement. Furthermore, knock-down of a subset of the identified RBPs led to the inhibition of the CP-induced increase of p27 mRNA levels. In conclusion, these results highlight substantial rearrangement between RBPs and p27 mRNA upon CP treatment and corroborate the importance of post-transcriptional control in cellular drug response.

2019-09-27 | PXD008498 | Pride

LC-MS by circHIPK3 probe method in human oral submucosal fibroblasts

Project description:To identify proteins to which circHIPK3 may bind and participate in the regulation of PDGF-BB-induced biological behavior in oral mucosal FBs, the circHIPK3 probe was designed for RNA pull-down experiment, and the proteins obtained from RNA pull-down were identified by silver staining, mass spectrometry and bioinformatics (COG, KEGG, PPI) analysis.

2025-05-13 | PXD062842 | Pride

Phospholipids with two polyunsaturated fatty acyl tails drive ferroptosi.

Project description:Phospholipids containing polyunsaturated fatty acyl tails (PL-PUFAs) are susceptible to lipid peroxidation by reactive oxygen species, lipoxygenases, and radical species. The accumulation of peroxidized lipids in cell membranes overwhelms endogenous lipid repair processes and triggers ferroptosis. We discovered that phospholipids with both PUFA tails (PL-PUFA2s) acted as key drivers of ferroptosis in numerous cancer cell lines, compared with phospholipids with a single PUFA tail (PL-PUFA1s), which were substantially less capable of inducing ferroptosis. We found that exogenously supplied phosphatidylcholine with two PUFA tails (PC-PUFA2) was rapidly incorporated into and remodeled membranes in cell lipids. Moreover, PC-PUFA2s were enriched upon free PUFA treatment, suggesting a key role in driving free-PUFA-initiated ferroptosis. We examined the protein-binding profile of PC-PUFA2 and found a specific interaction with the mitochondrial electron transport chain complex I. We confirmed that PC-PUFA2s accumulate in mitochondria and induce production of mitochondrial ROS, which then spread to the endoplasmic reticulum. Depletion of mitochondria through mitophagy eliminated the enhanced potency of PC-PUFA2s over PC-PUFA1s in driving ferroptosis, consistent with mitochondria being the key target of PC-PUFA2s. PC-PUFA2s are thus important lipid markers and drivers of ferroptosis and may serve as future biomarkers and therapeutic targets for modulating ferroptosis in pathological contexts.

2025-05-06 | PXD041993 | Pride

MG1655 Flagellar Regulators RNA-seq

Project description:This experiment contains RNA-seq data for a motile derivative of MG1655 and isogenic strains with deletions of each flagellar regulator: flhD, flhC, and fliA. All strains were grown at 37 degrees C in LB. After RNA purification, ribosomal RNA was removed using RiboZero and a library was made of remaining total RNA.

2014-08-01 | E-MTAB-2802 | biostudies-arrayexpress

The RNA pulldown of MEG3 to identify RNA-binding proteins

Project description:By using biotinylated MEG3 and streptavidin-labeled magnetic beads, identify the RNA-binding proteins of MEG3.

2025-06-30 | PXD062094 | Pride

14028s araC RNA-Seq

Project description:We used RNA-seq to determine the effects of AraC and arabinose on RNA levels genome-wide in S. enterica. Wild-type or delta araC mutant cells were grown in both the presence and absence of 0.2% L-arabinose. RNA-Seq libraries from two independent biological replicate samples were sequenced for (i) wild-type cells with no treatment, (ii) wild-type cells treated with arabinose, (iii) delta araC cells with no treatment, (iv) delta araC cells treated with arabinose. Comparisons were made between (i) and (ii) [analysis file name: Salmonella RNA-seq processed WT without arabinose vs WT with arabinose.xls], between (i) and (iii) [analysis file name: Salmonella RNA-Seq proessed no arabinose WT vs no arabinose delta araC.xls], and between (ii) and (iv) [analysis file name: Salmonella RNA-Seq processed arabinose WT vs arabinose delta araC.xls]. All analysis files are available from https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-1901/E-MTAB-1901.additional.1.zip

2013-10-04 | E-MTAB-1901 | biostudies-arrayexpress

Transcription profiling of Theiler stage 17 wild type mouse anterior vs posterior mouse sclerotome

Project description:This experiment was performed in order to identify transcriptional differences between the anterior- and posterior-halves of mouse sclerotome. Cells-derived from the anterior- and posterior-sclerotome-halves from maturing mouse somites were compared to identify transcripts that are differentially expressed between these two halves of the somite. c57b6-/- female mice were time-mated, and at 9.5-dpc embryos were harvested. Theiler stage 17 embryos were selected for dissection. A stripe of segmented paraxial mesoderm corresponding to somites SX-SXVIII (standard somite nomenclature) was dissected from one-side of an embryo. The most anterior-third of up to 7 sclerotomes within each sample were dissected and pooled in RNALater. RNA was isolated using RNeasy Micro RNA extraction spin columns (Qiagen). Reverse transcription and initial cDNA amplification was performed using 18 PCR cycles with the SMART cDNA system (Clontech). Amplified cDNA was then re-amplified and labeled using the GeneChip® IVT Labeling Kit (Affymetrix).

2006-11-16 | E-MEXP-913 | biostudies-arrayexpress

Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells

Project description:Syncytial skeletal muscle cells contain hundreds of nuclei in a shared cytoplasm. Using single nucleus RNA-sequencing (snRNAseq) of isolated nuclei from muscle fibers, we investigated nuclear heterogeneity and transcriptional dynamics in uninjured and regenerating muscle.

2020-10-07 | E-MTAB-8623 | biostudies-arrayexpress

Dissecting psa locus regulation in Yersinia pestis - RNA-seq

Project description:We compared RNA levels in wild-type Yersinia pestis with RNA levels in a mutant strain in which the psaE gene was deleted.

2019-10-04 | E-MTAB-8369 | biostudies-arrayexpress

Identification of ribosome proteins bound to IRES in hypoxia

Project description:Hypoxic conditions prompt internal ribosome entry site (IRES)-mediated translation of some of the hallmark cancer genes, such as VEGF. This translational switch is extremely vital for cell survival and tumor progression. Heterogeneity in ribosomes due to the diversity of ribosomal RNA (rRNA) and protein composition has been postulated to generate ‘specialized ribosomes’ that differentially regulate translation. A VEGF IRES sequence was used as bait to identify unique proteins bound at the IRES in breast cancer cells grown in hypoxia.

2021-01-06 | PXD019238 | 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