Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression analysis of inositol hexakisphosphate kinase 1 (IP6K1) knockout mouse embryonic fibroblasts

ABSTRACT: To investigate the biological significance of IP6K1 function we compared the gene expression profile of two mouse embryonic fibroblast (MEF) cell lines each derived from Ip6k1+/+ and Ip6k1-/- embryos. Results reveal downregulation of several biological processes upon the loss of IP6K1.

ORGANISM(S): Mus musculus

PROVIDER: GSE73612 | GEO | 2016/05/16

SECONDARY ACCESSION(S): PRJNA297429

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Gene expression analysis of inositol hexakisphosphate kinase 1 (IP6K1) knockout mouse embryonic fibroblasts

Project description:To investigate the biological significance of IP6K1 function we compared the gene expression profile of two mouse embryonic fibroblast (MEF) cell lines each derived from Ip6k1+/+ and Ip6k1-/- embryos. Results reveal downregulation of several biological processes upon the loss of IP6K1. Organism : Mus musculus , Agilent Gene Expression Whole Genome Mouse 4x44k (AMADID: 14868). Two biological replicates each of Ip6k1+/+ and Ip6k1-/- MEFs

2016-05-16 | E-GEOD-73612 | biostudies-arrayexpress

Deep transcriptome analysis of mouse embryonic fibroblast following simultaneous overexpression of Stella, Oct4 and Nanos2 (SON)

Project description:We constructed a polycistronic lentiviral vector to overexpress 3 germ cell specific genes (Stella, Oct4 and Nanos2) in mouse embryonic fibroblast (MEFs) and evaluated the transcriptome portrait in partially reprogrammed cells.We sequenced RNA samples from bulk cell population of two biological duplicates of MEF-GFP (control) and MEF-SON (overexpressed) 21 days post infection. Differential expression analysis of 50 M pair-end read per samples showed overexpression of neurogenesis, blood vessel and proliferation related genes and downregulation of chondroitin sulphate metabolic process, nitric oxide production and innate immune response genes.

2016-07-30 | GSE77351 | GEO

Gene expression analysis of wild-type and Beta-2-spectrin homozygous knockout (β2SP-/-) mouse embryonic fibroblasts

Project description:Gene expression profiling was carried out in wild and β2SP-/- (Sptbn1 -/-) mouse embryonic fibroblast (MEF) cells. Beta-2-spectrin (β2SP) is a dynamic intracellular non-pleckstrin homology (PH)-domain protein that belongs to a family of polypeptides that have been implicated in conferring cell polarity. Spectrins have been linked to multiple signaling pathways, including cell cycle regulation, DNA repair and TGFβ signaling. In this study, we report a major role of the TGFβ/Smad3 adaptor β2-Spectrin in conserving genomic integrity from alcohol-induced DNA damage and describe a novel pathway that protects genomes from genotoxic stresses.

2016-02-17 | GSE65987 | GEO

Deep transcriptome analysis of mouse embryonic fibroblast following simultaneous overexpression of Stella, Oct4 and Nanos2 (SON)

2016-07-30 | E-GEOD-77351 | biostudies-arrayexpress

Gene expression profiles of mouse embryonic fibroblasts (MEFs), induced cardiomyocytes (iCMs) and heart

Project description:Global gene expression patterns of the iCMs shift from a MEF state toward a cardiac-like phenotype by Gata4/Mef2c/Tbx5 (GMT) or GMT/miR-133 transduction at 3, 7 and 18 days after transduction (D3, D7 and D18) MiR-133 silenced fibroblast signatures in parallel with cardiac gene activation, and Snai1 overexpression inhibited the effects of miR-133-mediated cardiac reprogramming.

2014-07-03 | GSE56875 | GEO

Gene expression analysis of wild-type and Beta-2-spectrin homozygous knockout (Î²2SP-/-) mouse embryonic fibroblasts

Project description:Gene expression profiling was carried out in wild and Î²2SP-/- (Sptbn1 -/-) mouse embryonic fibroblast (MEF) cells. Beta-2-spectrin (Î²2SP) is a dynamic intracellular non-pleckstrin homology (PH)-domain protein that belongs to a family of polypeptides that have been implicated in conferring cell polarity. Spectrins have been linked to multiple signaling pathways, including cell cycle regulation, DNA repair and TGFÎ² signaling. In this study, we report a major role of the TGFÎ²/Smad3 adaptor Î²2-Spectrin in conserving genomic integrity from alcohol-induced DNA damage and describe a novel pathway that protects genomes from genotoxic stresses. Whole-transcriptome RNA sequencing of wild-type and Î²2SP knockout (Î²2SP-/-) mouse embryonic fibroblasts was carried out on an Illumina HiSeq 2000 sequencer. The raw data quality was assessed using a FastQC software. Adaptor presence was tested using Trimmomatic. The readings were then aligned to the NCBI mouse reference genome build 37.2 using the splice-aware aligner Tophat2 v2.0.10. Transcript quantification, normalization and assembly were carried out with Cufflinks. A gene model gtf file corresponding to the NCBI mouse reference genome build 37.2 was used in the quantification. Cuffdiff2, part of the Cufflinks suite of tools, was used to identify significant differences in gene expression profiles between the wild-type and Î²2SP-/- MEF cells.

2016-02-17 | E-GEOD-65987 | biostudies-arrayexpress

Analysis of the transcriptomic profile of WT mouse embryonic fibroblast (MEF WT) and Nf2-knockout mouse embryonic fibroblast (MEF Nf2 KO) cell lines

Project description:Analysis of the transcriptomic profile of WT mouse embryonic fibroblast (MEF WT) and Nf2-knockout mouse embryonic fibroblast (MEF Nf2 KO) cell lines

| PRJNA662370 | ENA

Transcription profiling of mouse embryonic fibroblasts (MEFs) trisomic for chromosomes 1, 13, 16 and 19

Project description:Aneuploidy, an incorrect chromosome number, is the leading cause of miscarriages and mental retardation in humans and is a hallmark of cancer. We examined the effects of aneuploidy on primary mouse cells by generating a series of cell lines that carry an extra copy of one of four mouse chromosomes. In all four trisomic lines proliferation was impaired and metabolic properties were altered. Immortalization, the acquisition of the ability to proliferate indefinitely, was also affected by the presence of an additional chromosome, with some chromosomes inhibiting immortalization while others accelerating the process. Our data indicate that aneuploidy decreases not only organismal but also cellular fitness and elicits traits that are shared between different aneuploid cells. Experiment Overall Design: The mRNAs from 9 different mouse embryo fibroblast (MEF) lines with a normal complement of chromosomes were compared to mRNAs from 1 MEF line with three copies of chromosome 1, 4 MEF lines with three copies of chrmosome 13, 3 MEF lines with three copies of chromosome 16 and 1 MEF line with three copies of chromosome 19.

2008-11-15 | E-GEOD-12501 | biostudies-arrayexpress

Proteomic response on ferroptosis induction via GPX4 KO in mouse embryonic fibroblasts

Project description:In the present study, we report proteome data of mouse embryonic fibroblasts (MEF cells) and immortalized mouse embryonic fibroblasts which are 4-OH-TAM-inducible Gpx4−/− (Pfa1 cells). Ferroptosis in Pfa1 cells was induced with Tamoxifen (Tam) addition and three timepoints were collected: 0h, 24h and 48h. Wild-type MEF cells were also measured as an alternative control without Tam addition. Raw data for HEK293 cells are provided as an independent quality control. MEF and Pfa1 cells (both kind gift from Marcus Conrad, Munich) were cultured in RPMI-1640 media (2 g/L glucose, 10% FBS, 2 mM Gibco GlutaMAX Supplement, 1% pen/strep) at 37C with 5% CO2 in a humidified incubator. Cells (300k) were seeded on Corning 100 mm tissue-culture treated culture dishes and incubated overnight. On the next day Pfa1 cells were treated with or without 1 µM Tam.

2023-04-12 | PXD040094 | Pride

Gene expression analysis of inositol hexakisphospahte kinase 1 (Ip6k1) knockout testes in juvenile mice

Project description:Ip6k1 knockout male mice are infertile and display a delay in the first wave of spermatogenesis. To understand the underlying basis of this delay, we compared the gene expression profiles of whole testes from 17 days postpartum (17dpp) and 26 days postpartum (26dpp) Ip6k1 wild type (Ip6k1+/+) and Ip6k1 knockout (Ip6k1-/-) mice. We observed deregulation of several biological processes in Ip6k1-/- testes compared with Ip6k1+/+ testes.

2021-06-20 | GSE153500 | 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