Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of OTULIN substrates

ABSTRACT: Lysates from WT- and C129A-Otulin expressing cells were each subjected to serial enrichment using FLAG-anti-linear polyubiquitin TUBEs (tandem ubiquitin binding elements) followed by FLAG-anti-K48-linked polyubiquitin TUBEs.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

SUBMITTER: Donald Kirkpatrick

PROVIDER: MSV000081959 | MassIVE | Mon Jan 22 12:10:00 GMT 2018

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Proteomic analysis of linear ubiquitination substrates based on NAEK-Ub probe in live cells

Project description:While linear ubiquitin plays critical roles in multiple cell signaling pathways, few substrates have been identified. Global profiling of linear ubiquitin substrates represents a significant challenge because of the low endogenous level of linear ubiquitination, the none-specific binding of linear polyubiquitin chain, and the high background interferences arising from heterogeneous ubiquitin linkages (e.g. K48-, K63-). We developed a bioorthogonal linear ubiquitin probe by site-specific encoding of a norbornene amino acid (NAEK) on ubiquitin. This probe facilitates covalent labeling of linear ubiquitin substrates in live cells and enables selective enrichment and identification of linear-ubiquitin modified proteins. we applied this probe in the profiling of substrates of linear ubiquitination in HEK293T cells and GSCs.

2022-02-11 | PXD031600 |

GNPS - Calcium flux control by Pacs1-Wdr37 promotes lymphocyte quiescence and lymphoproliferative diseases

Project description:S11537: anti-FLAG beads incubated with mouse B cell extract S11538: FLAG-Pacs1 purified from 293T cells on anti-FLAG beads S11536: FLAG-Pacs1 purified from 293T cells on anti-FLAG beads incubated with mouse B cell extract.

2021-02-03 | MSV000086799 | GNPS

LIN-41 RIP-Seq

Project description:FLAG-GFP tagged LIN-41 was immunoprecipitated using FLAG dynabeads (Sigma) from lysates of young adult C.elegans. After washing steps, bound fraction (IP) was eluted from beads and associated RNAs were isolated by using the Pico pure RNA isloation kit (Invitrogen)

2018-04-25 | GSE106814 | GEO

Genomewide occupancy of the synovial sarcoma-associated SYT-SSX2 oncoprotein in C2C12 myoblasts

Project description:Synovial sarcoma is a rare malignancy that is characterized by the presence of a chromosomal translocation t(X;18). This genetic abnormality results in the fusion of 2 transcriptional co-regulators, SYT and SSX, which have been shown to mediate transcriptional activation and repression, respectively. Although the fusion protein does not bind DNA directly, SYT-SSX2 is known to function through interaction with chromatin-modifying complexes. In this study, we wanted to determine the SYT-SSX2 occupancy across the whole genome in order to further characterize its function by identifying genes that may be deregulated by this protein. C2C12 myoblasts were infected with retrovirus carrying SYT-SSX2-HA-FLAG expression vector. Chromatin immunoprecipitation (ChIP) was performed on cell lysates with either control IgG antibody (Abcam) or anti-FLAG antibody (Sigma). Lysates from 2 independent infections were pooled and used to isolate control ChIP DNA (IgG). DNA from 2 independent FLAG ChIP experiments (each using lysates from 2 independent infections) was pooled for SYT-SSX2 ChIP.

2011-09-26 | E-GEOD-26564 | biostudies-arrayexpress

Integrative Genomics Positions MKRN1 as a Novel Ribonucleoprotein within the Embryonic Stem Cell Gene Regulatory Network

Project description:For identification of proteins that associate with Makorin1 (MKRN1) in RNA-dependent and RNA-independent manners, we affinity purified FLAG-tagged Makorin1 (MKRN1) from mouse embryonic stem cells constitutively expressing FLAG:MKRN1. Anti-FLAG control immunoprecipitations were performed from a FLAG vectrol control (FLAG:Ctrl) mouse embryonic stem cell line that did not express FLAG:MKRN1. Following FLAG immunoprecipitation, anti-FLAG beads from FLAG:MKRN1 and FLAG:Ctrl immunoprecipitations were split into separate tubes such that half of the beads were digested with 200Ã∞â≈ Ã≠Âµg/mL RNase A while the other half of the beads were undigested. RNase A-digested and undigested immunoprecipitates were subjected to LC-MS/MS analysis. Of the 48 RNA-related proteins previously identified to associate with FLAG:MKRN1, L1TD1, PABPC1, PABPC4, YBX1, IGF2BP1 and UPF1 were found to remain associated with FLAG:MKRN1 in the presence of RNase A.

2015-07-21 | PXD001291 | Pride

Identification of TULP3 protein interactions

Project description:Table S1: Anti-FLAG immunoprecipitation on HEK293T cell lysates stably expressing FLAG-TULP3 .

2020-10-22 | MSV000086357 | MassIVE

RNA immunoprecipitation to identify RHA-binding transcripts in HEK293 cells

Project description:Given that RHA regulates translation by binding a PCE located at the 5’ UTR of the target transcripts a genome-wide screen was performed to identify mRNAs that bind RHA in vivo. The results from four experiments with samples obtained in four independent RNA immunoprecipitations identified 375 transcripts that co-immunoprecipitate with FLAG RHA. Since N-terminal FLAG tagged RHA specifically co-immunoprecipitates PCE-containing mRNAs HEK293 cells were transfected with a CMV-FLAG-RHA construct. Cytoplasmic lysates were immunoprecipitated with anti-FLAG beads. RNA was extracted from the immunoprecipitate and used to probe a human Agilent expression arrays. An immunoprecipitation with cells transfected with empty FLAG plasmid was used as negative control.

2010-08-19 | E-GEOD-23688 | biostudies-arrayexpress

Identification and characterization of BEND2 as a novel and key regulator of meiosis during mouse spermatogenesis [BEND2_ChIPseq]

Project description:To characterize BEND2-binding sites on the genome, we conducted ChIP-seq analyses by using testicular lysates from FLAG-BEND2 KI mice. We found BEND2 preferentially binds to simple sequence repeats.

2022-06-01 | GSE189594 | GEO

piRNAs and transgenerational RNA interference protect essential genes from RNA silencing in C. elegans

Project description:This data series contains small RNA high-throughput sequencing data derived from cell lysates and FLAG::HRDE-1 immunoprecipitates (IP) after resetting RNAi in the presence or absence of piRNAs in C. elegans.

2015-06-30 | GSE63114 | GEO

Absolute quantification analysis of ubiquitin chains attached to Nrf1 purified from NGLY1-KO cells overexpressing Nrf1-FLAG with HA-FBS2.

Project description:We examined ubiquitin-linkages on Nrf1 purified from cell lysates of NGLY1-KO cells overexpressing Nrf1-FLAG with HA-FBS2. The ubiquitin linkage types were quantified using the LC-MS/MS-based absolute quantification method, ubiquitin parallel reaction monitoring (Ub-AQUA/PRM).

2024-08-06 | PXD053753 | 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