Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of Ikaros deletion on gene expression in CD4 T cells

ABSTRACT: The goal of this experiment is to define how lack of Ikaros impacts gene expression in mature CD4 T cells, both in the resting and activated state. To do this, a conditional knockout mouse model was generated using Cre/lox technology. The floxed allele was designed such that the last translated exon and 3' UTR of the Ikaros gene (Ikzf1) are deleted in mature T cells (mediated by distal Lck-driven Cre). CD4 T cells from mice with floxed alleles that did not express Cre (Cre-) and those that did express Cre (Cre+) were analyzed.

ORGANISM(S): Mus musculus

PROVIDER: GSE119067 | GEO | 2018/12/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Splenic B1 and B2 cells from mice with induced deletion of Ikaros

Project description:The experiment aimed at determining the genes that are under the control of the Ikaros transcription factor in mouse splenic B1 and B2 B lymphocyte subsets. To this aim, we used Ikf/f R26-CreERT2+ (Cre+) or Ikf/f R26-CreERT2- (Cre-) mice, which correspond to mice with floxed null alleles for Ikzf1 (Heizmann et al., JEM 210:2823-32, 2013) that were crossed with the R26-CreERT2 mice, which harbor a knock-in of the cDNA encoding the tamoxifen (TAM) inducible CreERT2 recombinase in the Rosa26 gene (Badea et al, J. Neurosci 23:2314-22, 2003). 6-8 week-old mice were injected daily with TAM for 3d (50mg/kg). Mice were sacrificed 10d after the first injection, and splenic B1 and B2 B cell populations sorted by flow cytometry. Splenic B1 and B2 cells from mice with induced deletion of Ikaros

2016-02-03 | GSE75827 | GEO

IKAROS re-expression modulates transcriptional networks in IKZF1-mutant Ph+ B-ALL [HiChIP]

Project description:With the goal to investigate tumor suppressor mechanisms regulated by IKAROS (IKZF1) in PH chromosome–positive B-cell acute lymphoblastic leukemia (B-ALL) harboring IKZF1 mutations. This dataset includes bulk RNA-seq profiles from human MXP5 and PDX2 cell lines, which were engineered to express doxycycline-inducible wild-type IKAROS (IK1) or an empty vector control. RNA was collected 24 hours post-induction to capture early transcriptional responses to IK1 re-expression. These data are part of a larger multi-omics study integrating RNA-seq, ChIP-seq, CUT&RUN, ATAC-seq, and HiChIP to define IKAROS-regulated transcriptional and chromatin networks in IKZF1-deficient Ph⁺ B-ALL.

2026-02-20 | GSE310891 | GEO

IKAROS re-expression modulates transcriptional networks in IKZF1-mutant Ph+ B-ALL [CUT&RUN]

2026-02-20 | GSE310959 | GEO

IKAROS re-expression modulates transcriptional networks in IKZF1-mutant Ph+ B-ALL [RNA-Seq]

2026-02-20 | GSE310958 | GEO

IKAROS re-expression modulates transcriptional networks in IKZF1-mutant Ph+ B-ALL [ChIP-Seq]

2026-02-20 | GSE310890 | GEO

IKAROS re-expression modulates transcriptional networks in IKZF1-mutant Ph+ B-ALL [ATAC-seq]

2026-02-20 | GSE310887 | GEO

RNA-SEQ analysis of CD4+ T cells in presence or absence of Ikaros.

Project description:We found by microarray analysis that Ikaros is critical to limit the expression of several pro-inflammatory genes during Th17 cell polarization. To unravel the role of Ikaros in the expression of pro-inflammatory genes without Th17 polarizing cytokines, we performed an RNA-seq analysis in naive CD4+ T cells and CD4+ T cells activated with anti-CD3+anti-CD28 antibodies (Th0 condition), from WT (Ikaros f/f CD4-Cre-) and Ikaros TKO mice (Ikaros f/f CD4-Cre+).

2021-04-26 | GSE157810 | GEO

Ikaros deficient mouse thymic lymphomas

Project description:This dataset comprises expression profiles from 3 thymic lymphomas from Ikaros deficient mice (IkL/L model, see Dumortier et al, Mol. Cell. Biol. 26, 209-220, 2006 for a description of the tumor model) and 3 thymic lymphomas from IkL/L mice that harbor a mutation of the Notch1 gene (deletion of floxed sequences comprising the promoter and exon 1 with the CD4-Cre transgene). The results from this experimpent is that the expression of Notch target genes was unexpectedly not altered in the tumors with the Notch1 deletion. This result is explained by the activation of a cryptic 3' Notch1 promoter in the deleted tumors, which leads to constitutive Notch1 activation. These results are described in the following publication: R Jeannet, J Mastio, B Macias-Garcia, A Oravecz, T Ashworth, AS Geimer-Lelay, B Jost, S Le Gras, J Ghysdael, T Gridley, T Honjo, F Radtke, J Aster, S Chan and P Kastner. Oncogenic activation of the Notch1 gene in mouse T-cell leukemia by deletion of its promoter. Blood, in press (2010) Primary thymic tumors from 3 IkL/L Notch1+/+ CD4-Cre+ mice (aged 18-20 weeks) were compared to similar tumors from 3 IkL/L Notch1f/f CD4-Cre+ mice (aged 8-10 weeks).

2010-09-03 | E-GEOD-23972 | biostudies-arrayexpress

Genome wide chromatin accessibility (ATAC-SEQ) in the presence or absence of Ikaros in CD4+ T cells.

Project description:We found that Ikaros is critical to limit the expression of pro-inflammatory cytokines in TCR/CD28-activated CD4+ T cells. To understand if Ikaros could modify the chromatin accessibility in regions controling the expression of these pro-inflammatory genes, we examined the chromatin state in naive CD4+ T cells and CD4+ T cells activated with anti-CD3+anti-CD28 antibodies for 1 and 2 days, from WT (Ikaros f/f CD4-Cre-) and Ikaros TKO mice (Ikaros f/f CD4-Cre+), using the ATAC-seq approach.

2021-04-26 | GSE157812 | GEO

Stage-specific control of early B cell development by the transcription factor Ikaros

Project description:Ikaros is an essential regulator of lymphopoiesis. Here, we studied the B-cell-specific function of Ikaros by conditional Ikzf1 inactivation in pro-B cells. B-cell development was arrested at an aberrant ‘pro-B’ cell stage characterized by increased cell adhesion and loss of pre-B cell receptor signaling. Ikaros was found to activate genes coding for pre-BCR signal transducers and to repress genes involved in the downregulation of pre-BCR signaling and upregulation of the integrin signaling pathway. Unexpectedly, derepression of Aiolos expression could not compensate for the loss of Ikaros in pro-B cells. Ikaros differentially controlled active chromatin at promoters and enhancers of repressed and activated target genes. Notably, Ikaros binding and target gene expression was dynamically regulated at distinct stages of early B-lymphopoiesis. 16 RNA-Seq samples in pre-proB cells (4 replicates, for each 2 controls and 2 experimental samples); 4 RNA-Seq samples in pro-B cells in Rag2-/- backgrounds (Ikzf1 deleted versus non deleted, 2 replicates each); 4 RNA-Seq samples in c-Kit high pro-B cells (Ikzf1 deleted versus non deleted, 2 replicates each); 4 RNA-Seq samples in pro-B cells (Ikzf1 deleted versus non deleted, 2 replicates each); 2 RNA-Seq samples pre-B cells wild type; 8 chromatin ChIP-Seq samples (4x H3K9ac, 4x H3K4me3, Ikzf1 deleted/non deleted, two replicates each).; 4 Transcription factor ChIP-Seq samples in pro-B cells; 1 Transcription factor ChIP-Seq samples in DP-T cells; 1 Transcription factor ChIP-Seq samples in pre-pro-B cells; 2 Mi-2b Chip-Seq samples (Ikzf1 deleted versus non deleted); 1 ChIP-Seq input track for pro-B cells; 1 ChIP-Seq input track for DP-T cells

2014-02-09 | E-GEOD-53595 | biostudies-arrayexpress

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