Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mouse - Identification of CTNND2 partners in synaptic fractions of P15 mouse brains

ABSTRACT: This project aims to identify CTNND2 partners in developing synapses

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Brain

SUBMITTER: Vanessa Masson

LAB HEAD: Damarys Loew

PROVIDER: PXD036487 | Pride | 2024-10-03

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	C5348FD.msf	Msf
	C5348FD_30112016.raw	Raw
	C5350FD.msf	Msf
	C5350FD_30112016.raw	Raw
	C6190FD.msf	Msf

Items per page:

1 - 5 of 13

Similar Datasets

Mouse - SRGAP2 partners in synaptic fractions of P15 mouse brains

Project description:This projects aims to identify the proteins that are in complex with SRGAP2 in developing synapses

2024-10-03 | PXD036488 | Pride

RagG interactome analysis in human breast MDA-MB-231 cells

Project description:RagC was immunoprecipitated from human breast cancer MDA-MB-231 cells treated or not with the Arp2/3 complex inhibitor, CK666, and the RagC interactome was analyzed by mass-spectrometry.

2023-09-04 | PXD027100 | Pride

ChIP-seq experiment of mouse embryonic stem cells (mESCs), assessing beta-catenin DNA binding in wild type mESCs and TCF/LEF quadruple knock-out mESCs.

Project description:Mouse embryonic stem cells (mESCs), derived from pre-implantation blastocyst cells, can be maintained in vitro in defined N2B27 medium supplemented with two chemical inhibitors for GSK3 and MEK (2i) and the cytokine leukemia inhibitory factor (LIF), which act synergistically to promote self-renewal and pluripotency. Many efforts have been devoted to identify genes that promote exit from the pluripotent state and the transition to a primed state of differentiation. One of the first identified players in this process was the Wnt/b-catenin effector TCF7L1 (previously referred to as TCF3), belonging to the family of four TCF/LEF transcription factors, which acts as pro-differentiation factor by repressing pluripotency genes. Of note, there is little evidence that the genetic abrogation of the mechanisms required for the exit from the pluripotent state is sufficient to enable self-renewal in the absence of 2iL. Here, we found that complete loss-of-function of Tcf7, Lef1, Tcf7l1 and Tcf7l2, the genes encoding for the four TCF/LEF transcription factors, (refered to as qKO) allows mESCs to become fully 2iL-independent and to propagate in basal N2B27. In addition to RNA-seq data deposited under accession number E-MTAB-10564, chromatin immunoprecipitation followed by deep DNA sequencing (ChIP-seq) has been performed in CHIR-stimulated mESCs. Here, the DNA binding landscape of β-catenin has been analyzed to assess its possible connection to TCF/LEF-mediated pluripotency.

2021-06-15 | E-MTAB-10575 | biostudies-arrayexpress

Glucocorticoid receptor profiling (ChIP-seq) in U2OS-GR cells 24 hours after hormone washout

Project description:We performed ChIP-seq targeting the glucocorticoid receptor (GR) in the U2OS-GR cell line. The cell line is derived from U2OS ATTC:HTB-96 and stably transfected with an expression construct for rat GR. The cells were treated with 100 nM dexamethasone for 4 hours, washed 2x with PBS and cultured in hormone-free medium for 24 hours before harvest.

2021-05-03 | E-MTAB-9914 | biostudies-arrayexpress

NeonGreen-POLQ knock-in in Human embryonic kidney 293 cells VS Human embryonic kidney 293 cells

Project description:Replication stress (RS) can lead to the formation of DNA double strand breaks (DSBs) and threatens genomic stability. Homologous recombination (HR) pathway is essential to prevent RS and repairs associated DSBs. Upon excessive RS or HR deficiency, DSBs can persist in mitosis, wherein DNA damage response and DSB repair are inhibited. Thus, the fate of DSBs remaining or arising in mitosis remains poorly understood. Here we unwind two distinct roles of the polymerase theta (Polθ) in the maintenance of genomic stability. First, by mass spectrometry and foci screening we show that, in interphase, Polθ interacts with HR proteins and its recruitment to IR-induced DSBs is highly dependent of HR pathway. Secondly, we identify a novel role of the Polθ in counteracting the deleterious effect of DSBs in mitosis. Contrariwise to its interphase recruitment, Polθ recruitment to mitotic DSBs is HR-independent and triggered by mitotic kinases activities. In response to RS or HR deficiency, Polθ localizes to DSBs throughout mitosis and forms nuclear bodies in the G1 daughter cells. In addition, Polθ localizes to centromeres and acentric fragments and activates the mitotic checkpoint. Conversely, Polθ deficiency leads to premature anaphase onset, resulting in an accumulation of mitotic abnormalities. Strikingly, the specific inhibition of Polθ in mitosis kills HR-deficient cells, identifying mitotic Polθ function as its key role in maintaining genome integrity. Our results pinpoint to the mitotic Polθ-mediated replication stress response pathway as a unique vulnerability of cancer cells, with great potential for further investigation.

2023-09-18 | PXD029585 | Pride

Enhancer Sequence Variants and Transcription Factor Deregulation Synergize to Construct Pathogenic Regulatory Circuits in B Cell Lymphoma (ChIP-Seq, FAIRE-Seq)

Project description:Most B cell lymphomas arise in the germinal center (GC), where humoral immune responses evolve from potentially oncogenic cycles of mutation, proliferation, and clonal selection. Although lymphoma gene expression diverges significantly from GC-B cells, underlying mechanisms that alter the activities of corresponding regulatory elements (REs) remain elusive. Here we define the complete pathogenic circuitry of human follicular lymphoma (FL), which activates or decommissions transcriptional circuits from normal GC-B cells and commandeers enhancers from other lineages. Moreover, independent sets of transcription factors, whose expression is deregulated in FL, target commandeered versus decommissioned REs. Our approach reveals two distinct subtypes of low-grade FL, whose pathogenic circuitries resemble GC-B or activated B cells. Remarkably, FL-altered enhancers also are enriched for sequence variants, including somatic mutations, which disrupt transcription factor binding and expression of circuit-linked genes. Thus, the pathogenic regulatory circuitry of FL reveals distinct genetic and epigenetic etiologies for GC-B transformation. Molecular profiling of follicular lymphoma, resting peripheral blood and tonsillar B cells using Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) and chromatin immunoprecipitation (H3ac and H3K27ac).

2015-01-15 | E-GEOD-62245 | biostudies-arrayexpress

Capture-C at paralogous gene loci in Drosophila embryos

Project description:Capture-C was performed on sonicated and amplified 3C libraries generated from nuclei isolated from fixed 3-18h Drosophila whole embryo samples. Capture-C was performed on wildtype and embryos with deletions or insertions at loop anchors/genes at the respective loci (scyl-chrb or tsh-tio). Capture-C was performed using two different Capture probe pools, one indicated as left (scyl, tsh, salm) and one as right (chrb, tio, salr).

2023-12-07 | E-MTAB-13271 | biostudies-arrayexpress

Tissue- and stage-specific Capture-C for selected TSS and CRM

Project description:Capture-C was performed on sonicated and amplified 3C libraries generated from nuclei isolated from 2-3h whole embryo samples or Mef2-/Elav-sorted nuclei from 6-8h and 10-12h embryo samples. Capture-C was performed on wildtype embryos. Capture-C was performed using two different Capture probe pools, one for TSS and one for CRM. TSS and CRM were hand curated for tissue- and stage-specific activity.

2023-12-07 | E-MTAB-9310 | biostudies-arrayexpress

A unique chromatin complex occupies young alpha-satellite arrays of human centromeres

Project description:Using high-resolution chromatin immunoprecipitation (ChIP) of centromere components and clustering of sequence data we find that specific dimeric alpha-satellite units shared by multiple individuals dominate functional human centromeres. We have analyzed the chromatin landscape of the human genome using paired-end MNase-seq

2015-02-12 | E-GEOD-60951 | biostudies-arrayexpress

Chromatin immunoprecipitation of TCF4 in human LS174AT cells using Nimblegen human genome-wide chips

Project description:genome-wide ChIP-on-chip against TCF4 in LS174T cells, performed on NimbleGen Systems, Inc. human genome-wide 38-chip, hg17 array set followed by verification using biological replicates on a dedicated design.

2008-02-13 | E-TABM-402 | 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