Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of defective proteins trapped by TanGIBLE

ABSTRACT: To identify an uncharacterized endogenous defective protein pool, we immunoprecipitated Flag-tagged TanGIBLE from HeLa cell extracts, and co-immunoprecipitated proteins werer subjected to LC-MS/MS analysis.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell

SUBMITTER: Takuya Tomita

LAB HEAD: Yasushi Saeki

PROVIDER: PXD057470 | Pride | 2024-12-25

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20240110_Evosep_40SPD_Kawahara_lab.msf	Msf
	20240110_Evosep_40SPD_Kawahara_lab.pep.xml	Pepxml
	20240110_Evosep_40SPD_Kawahara_lab_01.raw	Raw
	20240110_Evosep_40SPD_Kawahara_lab_02.raw	Raw
	20240110_Evosep_40SPD_Kawahara_lab_03.raw	Raw

Items per page:

1 - 5 of 18

Similar Datasets

Single-nucleus RNA-seq of adult female and male mouse livers for sex-biased gene expression analyses

Project description:To obtain new insight into the sexual dimorphism of mammalian livers, single-nucleus RNA-seq was performed on the liver samples from two female and two male adult mice. The single-nucleus libraries were generated on the 10X Chromium Next GEM Single Cell 3ʹ platform and sequenced on Illumina NextSeq 550. We used the data to understand the heterogeneity and sex-biased gene expression of liver cell types. The data revealed significant sex differences primarily focused on hepatocytes. Specifically, from the sex-biased genes detected at the bulk tissue level, we observed that male-biased genes are more highly expressed in male hepatocytes, and female-biased genes are more highly expressed in female hepatocytes.

2023-08-03 | E-MTAB-12180 | biostudies-arrayexpress

Role of Fnr1 and Fnr3 in transcriptional regulation under oxygen limitation in Herbaspirillum seropedicae

Project description:To determine the direct promoter targets of Fnr proteins, we correlated transcriptional changes observed in single fnr1 and fnr3 mutants (E-MTAB-5741) with ChIP-Seq analysis, taking advantage of C-terminally 3xFlag fnr alleles engineered into the H. seropedicae genome. ChIP-seq data were obtained from cultures grown under limited oxygen availability. Using this approach, DNA-binding targets for the H. seropedicae Fnr1 and Fnr3 proteins were unambiguously revealed and correlated with transcript profiles to determine the specific regulons of each protein.

2018-02-26 | E-MTAB-6395 | biostudies-arrayexpress

SPIN - Species by Proteome INvestigation

Project description:Species determination based on genetic evidence is an indispensable tool in archaeology, forensics, ecology, and food authentication. Most available analytical approaches involve compromises with regard to the number of detectable species, high cost due to low throughput, or a labor-intensive manual process. Here, we introduce “Species by Proteome INvestigation” (SPIN), a shotgun proteomics workflow capable of querying over 150 mammalian species by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Rapid peptide chromatography and data-independent acquisition (DIA) with throughput of 200 samples per day reduce expensive MS time, whereas streamlined sample preparation and automated data interpretation save labor costs. We confirmed the successful classification of known reference bones, including domestic species and great apes, beyond the taxonomic resolution of the conventional peptide mass fingerprinting (PMF)-based Zooarchaeology by Mass Spectrometry (ZooMS) method. In a blinded study of degraded Iron-Age material from Scandinavia, SPIN produced reproducible results between replicates, which were consistent with morphological analysis. Finally, we demonstrated the high throughput capabilities of the method in a high-degradation context by analyzing more than two hundred Middle and Upper Palaeolithic bones from Southern European sites with late Neanderthal occupation. While this initial study was focused on modern and archaeological mammalian bone, SPIN will be open and expandable to other biological tissues and taxa.

2022-05-19 | PXD024487 | Pride

ChIP-Seq of Myf5, MyoD, Snai1, HDAC1, HDAC2, E47 and empty vector controls in mouse skeletal myoblasts or myotubes

Project description:In skeletal myogenesis, the transcription factor MyoD activates distinct transcriptional programs in progenitors compared to terminally differentiated cells. Using ChIP-seq and gene expression analyses, we show that in primary myoblasts, Snail-HDAC1/2 repressive complex bind and exclude MyoD from its targets. Notably, Snail binds E-box motifs that are G/C-rich in their central dinucleotides, and such sites are almost exclusively associated with genes expressed during differentiation. By contrast, Snail does not bind the A/T-rich E-boxes associated with MyoD targets in myoblasts. Thus, Snai1-HDAC1/2 prevents MyoD occupancy on differentiation-specific regulatory elements and the change from Snail- to MyoD-binding often results in enhancer switching during differentiation. Furthermore, we show that a regulatory network involving Myogenic Regulatory Factors (MRFs), Snail/2, miR-30a and miR-206 acts as a molecular switch that controls entry into myogenic differentiation. Together, these results reveal a regulatory paradigm that directs distinct gene expression programs in progenitors versus terminally differentiated cells. Genome wide binding sites of various transcription factors and chromatin modifiers in muscle cells

2012-07-04 | E-GEOD-24852 | biostudies-arrayexpress

Snail regulates MyoD binding-site occupancy to direct enhancer switching and differentiation-specific transcription in myogenesis

Project description:This SuperSeries is composed of the following subset Series: GSE24811: Time Series of Mouse skeletal muscle cell differentiation GSE24852: ChIP-Seq of MyoD, Myf5, Snai1, HDAC1, HDAC2, E47 and empty vector controls in mouse skeletal myoblasts or myotubes GSE38236: RNA-Seq of si-Snai1, si-Snai2, si-Snai1/2 and si-Scrambled treated myoblasts Refer to individual Series

2012-07-04 | E-GEOD-24904 | biostudies-arrayexpress

ChIP-Seq of Pax7 and Pax3 in myoblasts

Project description:Examination of binding locations of Pax3 and Pax7 in primary myoblasts UCSC track hub available at: http://www.ogic.ca/projects/Soleimani_2012_Pax7_hub/hub.txt For details on viewing the track hub in the UCSC Genome Browser: http://altair.dartmouth.edu/ucsc/goldenPath/help/hgTrackHubHelp.html#View 3 Samples (Control, Pax7 ChIP, Pax3 ChIP)

2012-05-22 | E-GEOD-25064 | biostudies-arrayexpress

CT26 sorted in vivo tumor cells with Trex1 KO

Project description:The DNA exonuclease TREX1 degrades endogenous cytosolic DNA. Cytosolic DNA triggers the cGAS/STING pathway which increases type I interferon. To investigate the physiological significance of TREX1 loss on in vivo tumor growth, we implanted control and TREX1-deficient CT26 tumor cells into immunocompetent BALB/c hosts.Tumor cells were collected 7 days after tumors reached around 200mm3.

2024-03-12 | E-MTAB-13816 | biostudies-arrayexpress

Interactome analysis of GST-UFD1-NBM

Project description:GST pull-down assay using crude extracts from HCT116 cells to analyze the selectivity of the UFD1-NBM peptide in a cellular context.

2025-06-03 | PXD063521 | Pride

ChIP-seq of Mycobacterium smegmatis PafBC to identify in vivo binding sites

Project description:We aimed to determine the binding sites of the putative transcriptional regulator PafBC under DNA damage stress induced by mitomycin C or under oxidative stress induced by hydrogen peroxide. Therefore, we chose a ChIP-seq approach, crosslinking cells before PafBC-DNA complexes were immunoprecipitated with a PafBC-specific antibody.

2018-06-17 | E-MTAB-6503 | biostudies-arrayexpress

Study of RFX1 and RFX3 binding sites in the mouse genome

Project description:The aim of the study was to identify RFX1 and RFX2 binding sites in mouse pancreatic beta cells. Chromatin immunoprecipitation experiments were performed with the mouse MIN6 beta cell line and antibodies raised against RFX1 and RFX3. Immunoprecipitated DNA was sequenced using the Genome Analyzer II (Illumina). Antibodies were described in Reith W, Ucla C, Barras E, Gaud A, Durand B, Herrero-Sanchez C, Kobr M, Mach B : RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins. Mol Cell Biol 1994;14:1230–1244

2015-08-22 | E-GEOD-72272 | 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