Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

IFlpMosaic enable the multispectral barcoding and high-throughput comparative analysis of mutant and wildtype cells.

ABSTRACT: In order to understand gene function, cells mutated for a gene need to be compared with normal cells. In most biomedical studies this comparative analysis is carried out with cells present in different animals and therefore not experiencing the same microenvironment or epigenetic changes. Here we present a large set of new genetic tools and mouse lines, that enable the Flp recombinase-dependent ratiometric induction and single cell clonal tracking of multiple fluorescently labelled normal and Cre-mutant cells, from distinct or the same progenitor cells. The labelled cells can be profiled in situ by multispectral imaging, or by FACS and scRNA-seq. With these new tools, normal and mutant cells can be ratiometrically induced and multispectrally barcoded within the same temporal window and tissue microenvironment. This enables a better understanding of how induced genetic mutations affect the biology of single cells with higher accuracy and reliability during tissue development, homeostasis, or disease.

ORGANISM(S): Mus musculus

PROVIDER: GSE257723 | GEO | 2024/09/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Sequencing of freshly produced RNA following exposure of cells to DNA damage-inducing UV mimetic 4-hydroxyaminoquinolone (4-NQO)

Project description:We used Illumina-HiSeq4000 to sequence 4sU-labelled RNA samples isolated from unchallenged and DNA damaged HeLa Flp-In cells, which revealed the nature of transcriptional response folowing genotoxic stress and the contribution of P-TEFb kinase in DNA damage-induced gene transcription.

2019-04-09 | GSE110272 | GEO

iFlpMosaic enable the multispectral barcoding and high-throughput comparative analysis of mutant and wildtype cells.

Project description:iFlpMosaic enable the multispectral barcoding and high-throughput comparative analysis of mutant and wildtype cells.

| PRJNA1080217 | ENA

CD74-NRG1 fusion as an bona fide oncogene

Project description:3' RNA sequencing results of Rosa26CD74-NRG1/Flp mice (murine embryonic fibroblasts, tumor and normal tissue)

2022-02-28 | GSE184004 | GEO

C. elegans L4 hypodermal SLAM-ITseq

Project description:To adapt SLAM-ITseq for Caenorhabditis elegans, we inserted a codon-optimized version of the Toxoplasma gondii UPRT gene downstream of a FRT-flanked mCh::his-58 cassette and under control of the strong and ubiquitous eft-3 promoter. We introduced a single copy of this construct into the C. elegans genome and crossed the resulting line with a dpy-7p::FLP driver. FLP-dependent expression of UPRT was confirmed by Western blotting (strain BN1190). As a proof of concept, we exposed animals to 4-TU from L3 to L4 stage and purified total RNA. RNA from animals without FLP expression was used to control for UPRT-independent labeling strain BN1158). RNA was alkylated with iodoacetamide, which leads to a T>C conversion of 4-TU-labeled positions during cDNA synthesis, and subjected to deep sequencing (see Materials and Methods). We confirmed that the presence of FLP and UPRT did not affect gene expression. Comparing the T>C conversion rate per gene revealed a significant increase in nematodes expressing UPRT in the hypodermis. Next, we performed a beta-binominal test to identify genes that were significantly labelled across all replicas, which retrieved 197 genes (p<0.003; FDR<0.1 after adjustment for multiple comparisons). Original SLAM-ITseq reference: Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Ameres SL, Miska EA (2018) SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting. Development 145 (13). doi:10.1242/dev.164640

2022-12-31 | GSE192419 | GEO

Monosome and disome profiling of Flag-STAU1 Flp-In 293 T-REx cells

Project description:Monosome and disome profiling was performed on Flag-STAU1 Flp-In 293 T-REx to study the causes of ribosomal collisions, and whether this may be modulated by the presence/absence of Staufen-1. Cells were treated with either an siRNA targeting STAU1 transcript (4x samples) or a control siRNA (2x samples). Two of the four samples treated with the STAU1 siRNA had siRNA-resistant STAU1 mRNA expression induced by doxycycline (rescue). Sequencing libraries from monosome and disome fractions were generated in parallel from the same samples. Note that unique molecular identifiers/random barcodes (UMIs/RBCs) were included in the sequencing experiment. Each UMI has been moved to the fastq read name of each read. For example \\"xxxxxxrbc:AGCCAAT\\" in the read name signifies that the given read had a UMI of \\"AGCCAAT\\". Using these UMIs, PCR duplicates can be removed with UMI-Tools following read alignment.

2023-04-30 | E-MTAB-9669 | biostudies-arrayexpress

Stable and inducible expression of Fbxo25 in Flp-In-293 cells: control vs. tetracycline treatment

Project description:Expression profile of human Flp-In-293-WT-FBXO25 or Flp-In-293-∆F-FBXO25 cells comparing non treated cells vs. tetraciclyne treated for 24 and 48 hours. Flp-In-293-∆F-FBXO25 cells when induced express the non functional protein (without F-box domain). The objective of the study was to identify genes up or down-regulated when Fbxo25 wild-type or Fbxo25 lacking F-box domain is superexpressed.

2012-05-15 | GSE37380 | GEO

Genome-wide FLP/MYB88 binding sites in Arabidopsis thaliana

Project description:FLP and MYB88 are two paralogous MYB proteins, regulating the symmetric division of guard mother cell during Arabidopsis stomatal development. To understand their molecular functions, we performed genome-wide identification of FLP/MYB88 binding targets using ChIP-chip with FLP/MYB88 antibody. By comparing ChIP-chip between wild-type and flp-1 myb88 lines, a total genes were identified as putative direct targets for FLP/MYB88.

2010-09-01 | GSE19763 | GEO

SILAC APMS analysis of Pih1D2 interactome

Project description:To get insights into the function of Pih1D2 protein, we characterized its partners by performing a proteomic analysis in human cells. We fused this domain to GFP and stably expressed it in HeLa cells using site-specific integration with the Flp-In system. Following differential labeling of GFP-Pih1D2 and control cells with isotopically labelled amino-acids (SILAC), whole cell extracts were immuno-precipitated (IP) with anti-GFP antibodies and immunoprecipitates were subjected to quantitative mass-spectrometry analysis. SILAC labels: K0R0 control Hela H9 vs K4R6 x-FLAG- GFP- Pih1D2

2018-06-10 | PXD009520 | Pride

SILAC APMS analysis of DNAAF2 interactome

Project description:To get insights into the function of DNAAF2 protein, we characterized its partners by performing a proteomic analysis in human cells. We fused this domain to GFP and stably expressed it in HeLa cells using site-specific integration with the Flp-In system. Following differential labeling of GFP- DNAAF2 and control cells with isotopically labelled amino-acids (SILAC), whole cell extracts were immuno-precipitated (IP) with anti-GFP antibodies and immunoprecipitates were subjected to quantitative mass-spectrometry analysis. SILAC labels: K0R0 control Hela H9 vs K4R6 x-FLAG- GFP- DNAAF2

2018-06-10 | PXD009501 | Pride

SILAC APMS analysis of Pih1D3 interactome

Project description:To get insights into the function of Pih1D3 protein, we characterized its partners by performing a proteomic analysis in human cells. We fused this domain to GFP and stably expressed it in HeLa cells using site-specific integration with the Flp-In system. Following differential labeling of GFP-Pih1D3 and control cells with isotopically labelled amino-acids (SILAC), whole cell extracts were immuno-precipitated (IP) with anti-GFP antibodies and immunoprecipitates were subjected to quantitative mass-spectrometry analysis. SILAC labels: K0R0 control Hela H9 vs K4R6 x-FLAG- GFP- Pih1D3

2018-06-10 | PXD009499 | 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