PXD070150

PXD070150 is an original dataset announced via ProteomeXchange.

Title	RNA pull down experiment for vA-202 (ANAPC1P2) lncRNA
Description	This study aimed to identify protein interaction partners of the lncRNA vA-202 using an RNA pull-down approach followed by mass spectrometry. Biotinylated vA-202 RNA was generated by in vitro transcription incorporating biotin-14-CTP. For each pull-down reaction, 400 µg of whole-cell lysate (in a total volume of 100 µL) was incubated with 1 µg of biotinylated RNA in the presence of protease inhibitor cocktail (PIC), RNaseOUT, and 2× TENT buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 500 mM NaCl, 0.5% Tween-20), supplemented with IP lysis buffer (25 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% NP-40, 5% glycerol). The mixture was rotated at 4 °C for 2 hours. In parallel, streptavidin magnetic beads were washed three times with PBST (PBS + 0.1% Tween-20) and maintained on ice. The RNA-protein complexes were captured by adding the reaction mixture to the pre-washed magnetic beads and incubated for an additional 2 hours at 4 °C. Beads were then washed five times with PBST and twice with 100 mM ammonium bicarbonate. Bound proteins were eluted by incubating the beads in 0.1% RapiGest supplemented with 5 mM DTT at 60 °C for 30 minutes. The eluates were collected for downstream proteomic processing and LC-MS/MS analysis. Two controls were included: (i) a pull-down using an unrelated RNA (p-XEF) and (ii) a beads-only control (no RNA). All pull-down experiments were performed in triplicate.
HostingRepository	PRIDE
AnnounceDate	2026-05-25
AnnouncementXML	Submission_2026-05-24_16:18:16.529.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Amruta Jadhav
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-31 06:14:00	ID requested
⏵ 1	2026-05-24 16:18:17	announced

10.1093/nar/gkag375;

Jadhav AR, Sahoo S, Kuber YL, Hatwar K, Varanwal A, Tanwar K, Palwankar S, Chatrasal G, Mali AM, Bapat SA, genes) contribute to genetic and functional diversity of the human genome. Nucleic Acids Res, 54(8):(2026) [pubmed]

submitter keyword: Human, RNA pull down, Orbutrap MS

Dr. Sharmila A. Bapat
contact affiliation	National Centre for Cell Science, SPPU, Pune, India.
contact email	sabapat@nccs.res.in
lab head
Amruta Jadhav
contact affiliation	National centre for cell science, Pune, India
contact email	amrutaj355@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD070150

PRIDE project URI

• PRIDE
  1. PXD070150
     1. Label: PRIDE project
     2. Name: RNA pull down experiment for vA-202 (ANAPC1P2) lncRNA