Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microprotein knockout in rescue cell lines and control conditions

ABSTRACT: Microprotein knockout in rescue cell lines and control conditions

PROVIDER: PRJNA971880 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Microprotein knockout in rescue cell lines and control conditions

Project description:RNA-seq sequencing was carried out to investigate which expression alterations were induced by treatment with sgRNAs targeting the sORFs/microproteins of interest. To test whether any of these changes could be reversed in the microprotein rescue-GFP fusion cells, transcriptional alterations of rescue and parental cells were compared.

2023-10-09 | GSE232375 | GEO

Rap1a GTPase mVSM Knockout vs. Rescue Expression

Project description:This SuperSeries is composed of the following subset Series: GSE24749: Rap1a GTPase mVSM Knockout vs. Rescue miRNA Expression GSE25702: Rap1a GTPase mVSM Knockout vs. Rescue mRNA Expression Refer to individual Series

2011-04-13 | E-GEOD-25703 | biostudies-arrayexpress

Microprotein-Encoding RNA Regulation in Cells Treated with Pro-inflammatory and Pro-Fibrotic Stimuli (Ribo-Seq colon cell lines)

Project description:Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously unannotated microprotein-coding small open reading frames (smORFs). Most functional microproteins were chosen for characterization because of their evolutionary conservation. However, one example of a non-conserved immunomodulatory microprotein in mice suggests that strict sequence conservation misses some intriguing microproteins. Here, we examine the ability of gene regulation to identify human microproteins with potential roles in inflammation or fibrosis of the intestine. To do this, we collected ribosome profiling data of intestinal cell lines and peripheral blood mononuclear cells (PBMCs), and then used gene expression of microprotein-encoding transcripts to identify strongly regulated microproteins, including several examples of microproteins that are only conserved with primates. This approach reveals a number of new microproteins worthy of additional functional characterization, and provides a dataset that can be queried in different ways to find additional gut microproteins of interest.

2024-10-23 | GSE269371 | GEO

Microprotein-Encoding RNA Regulation in Cells Treated with Pro-inflammatory and Pro-Fibrotic Stimuli (RNA-Seq colon cell lines)

2024-10-23 | GSE269374 | GEO

The microprotein Minion controls cell fusion and muscle formation

Project description:These findings establish minion as a novel microprotein required for muscle development, and define a two-component program for the induction of mammalian cell fusion.

2017-05-19 | GSE97764 | GEO

Analysis of gene expression in the "clock rescue" and rpaA- "clock rescue" strains of Synechococcus elongatus PCC7942 with RNA sequencing in light/dark conditions

Project description:The transcription factor RpaA is the master regulator of circadian transcription in cyanobacteria, driving genome-wide oscillations in mRNA abundance. Deletion of rpaA has no effect on viability in constant light conditions, but renders cells inviable in cycling conditions when light and dark periods alternate. We investigated the mechanisms underlying this viability defect. We performed RNA-seq experiment using the rpaA- “clock rescue” and “clock rescue” strains and we show that the rpaA- “clock rescue” strain is defective in transcription of genes crucial for utilization of carbohydrate stores at night.

2017-02-15 | GSE89999 | GEO

CRISPR Knockout Screen to Identify Mechanisms of Rescue of DDX41-deficient Hematopoietic Progenitors

Project description:DDX41 is essential for the survival and proliferation of mouse hematopoietic progenitor cells (HPC). To identify mechanisms to rescue the survival of DDX41-deficient HPC, we conducted a genome-wide CRISPR Knockout Screen in DDX41-deficient and wild-type mouse bone marrow lineage-negative cells.

2022-06-01 | GSE178894 | GEO

EZH2 knockout and rescue in WCM154 NEPC organoid model. [RNA-Seq]

Project description:EZH2 knockout and rescue in WCM154 NEPC organoid model. [RNA-Seq]

| PRJNA1077935 | ENA

PD-1 Knockout Engineered T Cells for Advanced Colorectal Cancer with MSI high expression

Project description:Interventions: experimental group :PD-1 Knockout Engineered T Cells Primary outcome(s): Number of participants with Adverse Events and/or Dose Limiting Toxicities as a Measure of Safety and tolerability of dose of PD-1 Knockout T cells using Common Terminology Criteria for Adverse Events (CTCAE v4.0) in patients Study Design: historical control

| 2662961 | ecrin-mdr-crc

A nitrogen source-regulated microprotein confers an alternative mechanism of G1/S transcriptional activation in budding yeast

Project description:Commitment to cell division at the end of G1 phase, termed Start in the budding yeast Saccharomyces cerevisiae, is strongly influenced by nutrient availability. To identify new dominant activators of Start that might operate under different nutrient conditions, we screened a genome-wide ORF overexpression library for genes that bypass a Start arrest caused by absence of the G1 cyclin Cln3 and the transcriptional activator Bck2. We recovered a hypothetical gene YLR053c, renamed NRS1 for Nitrogen-Responsive Start regulator 1, which encodes a poorly characterized 108 amino acid microprotein. Endogenous Nrs1 was nuclear-localized, restricted to poor nitrogen conditions, induced upon mTORC1 inhibition, and cell cycle-regulated with a peak at Start. NRS1 interacted genetically with SWI4 and SWI6, which encode subunits of the main G1/S transcription factor complex SBF. Correspondingly, Nrs1 physically interacted with Swi4 and Swi6 and was localized to G1/S promoter DNA. Nrs1 exhibited inherent transactivation activity and fusion of Nrs1 to the SBF inhibitor Whi5 was sufficient to suppress other Start defects. Nrs1 appears to be a recently evolved microprotein that rewires the G1/S transcriptional machinery under poor nutrient conditions.

2021-08-25 | GSE179366 | GEO

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