Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Youn_et_al_RNAbodies_SAINT3105_Set3

ABSTRACT: This set of submissions contains the mass spectrometry files for the manuscript by Ji-Young Youn et al. that describes the high-density proximity mapping of RNA bodies. BioID experiments were performed from Flp-In T-REx HEK293 cells and MS files were acquired on Orbitrap Elite and Orbitrap Velos. Different MassIVE submissions corresponding to SAINT 3105 (see list below) have been made and this is set 3.

INSTRUMENT(S): LTQ Velos, LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Anne-Claude Gingras

PROVIDER: MSV000081413 | MassIVE | Fri Aug 04 14:41:00 BST 2017

SECONDARY ACCESSION(S): PXD007201

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Publications

Linking long noncoding RNA to drug resistance.

Smallegan Michael J MJ Rinn John L JL

Proceedings of the National Academy of Sciences of the United States of America 20191010 44

PMID: 31601736

Similar Datasets

Youn_et_al_RNAbodies_SAINT3105_Set1

Project description:This set of submissions contains the mass spectrometry files for the manuscript by Ji-Young Youn et al. that describes the high-density proximity mapping of RNA bodies. BioID experiments were performed from Flp-In T-REx HEK293 cells and MS files were acquired on Orbitrap Elite and Orbitrap Velos.

2017-08-04 | MSV000081411 | MassIVE

Youn_et_al_RNAbodies_SAINT3105_Set2

2017-08-04 | MSV000081412 | MassIVE

Youn_et_al_RNAbodies_SAINT3108_MSPLIT_DDA (PAIRED with MSV000081419)

Project description:This set of submissions contains the mass spectrometry files acquired using Data-Dependent Acquisition mode (DDA), which were paired with Data-Independent Acquisition mode (DIA) files (MSV000081419) for the manuscript by Ji-Young Youn et al. that describes the high-density proximity mapping of RNA bodies. These DDA files were used to generate spectral library in MSPLIT analysis of both DDA and DIA files. The paired SAINT 3108 set entails BioID experiments of stress granule and Processing-body baits expressed in Flp-In T-REx HEK293 cells, treated or untreated with sodium arsenite during labeling period.

2018-01-17 | MSV000081948 | MassIVE

Youn_et_al_RNAbodies_SAINT3090_MSPLIT_DDA (PAIRED with MSV000081414)

Project description:This set of submissions contains the mass spectrometry files acquired using Data-Dependent Acquisition mode (DDA), which were paired with Data-Independent Acquisition mode (DIA) files (MSV000081414) for the manuscript by Ji-Young Youn et al. that describes the high-density proximity mapping of RNA bodies. These DDA files were used to generate spectral library in MSPLIT analysis of both DDA and DIA files. The paired SAINT 3090 set entails APMS experiments of stress granule baits treated or untreated briefly with sodium arsenite and these were were performed from Flp-In T-REx HEK293 cells and MS files were acquired on AbSciex Triple TOF 6600 instrument in data-independent acquisition mode.

2018-01-17 | MSV000081947 | MassIVE

Youn_et_al_RNAbodies_SAINT3073_MSPLIT_DDA (Paired with MSV000081422)

2018-01-17 | MSV000081943 | MassIVE

Youn_et_al_RNAbodies_SAINT3112_MSPLIT_DDA (PAIRED with MSV000081426)

2018-01-17 | MSV000081945 | MassIVE

Lambert_TBX2_characterization_HEK293_P82_VS18

Project description:This set of submissions contains the mass spectrometry files by Jean-Philippe Lambert et al. that describes the functional characterization of TBX2. AP-MS and BioID experiments were performed from Flp-In T-REx HEK293 cells and MS files were acquired on 5600 TripleTOF mass spectrometers. Different MassIVE submissions corresponding to SAINT Task Results (see list below) have been made; this README file pertains to all submissions. For questions, please contact Jean-Philippe Lambert (Jean-Philippe.Lambert@crchudequebec.ulaval.ca).

2020-12-17 | MSV000086613 | MassIVE

Youn_et_al_RNAbodies_SAINT3115

Project description:Youn et al. High-density proximity mapping reveals the subcellular organization of mRNA-associated granules and bodies . Files related to SAINT 3115.

2017-08-06 | MSV000081415 | MassIVE

Piette_Hsp70-JPD_P77_VS7_VS16_APMS_DDA

Project description:This dataset consists of 232 raw MS files and associated peak lists and result files, acquired on a TripleTOF 5600 mass spectrometer operated in Data Dependent Acquisition mode. DDA files were used for library generation using MSPLIT-DIA and MSGFDB (see details below), but this deposition lists the identification and SAINT scoring using iProphet. The files are associated with a manuscript in Molecular Cell by Piette et al. that determines the protein-protein and proximity interaction landscape of every human Hsp70 and J-Domain Protein. Five separate MassIVE submissions are associated with this dataset.

2021-01-19 | MSV000086725 | MassIVE

Janer_et_al_ESYT1_mitochondria_ER_contacts_P129

Project description:This submission contains 24 raw mass spectrometry files and associated peak lists and result files for the manuscript by Alexandre Janer et al. that describes the proximity interactors of SMP-domain containing proteins, as well as an ER marker, an outer mitochondrial membrane marker and a tether between ER and mitochondria. BioID experiments were performed from Flp-In T-REx 293 cells and MS files were acquired on TripleTOF, Orbitrap Elite and Orbitrap Velos. MassIVE submissions corresponding to SAINT 6368 have been made. Samples were generated by Kathleen Daigneault, Mari Aaltonen and Hana Antonicka, affinity purification and mass spectrometric acquisition was performed by Zhen-Yuan Lin. Analysis was performed by Hana Antonicka under the supervision of Anne-Claude Gingras. Eric A. Shoubridge (eric.shoubridge@mcgill.ca) is the corresponding authors of the manuscript; Hana Antonicka (hana.antonicka@mcgill.ca) should be contacted for questions on this dataset.

2023-10-12 | MSV000093090 | MassIVE

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