{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD079777/20230911_CO_1128ThSt_R10B.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD079777/20230911_CO_1128ThSt_R09B.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD079777/20230911_CO_1128ThSt_R08A.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD079777/20230911_CO_1128ThSt_R08B.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD079777/20230911_CO_1128ThSt_R07B.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD079777/20230911_CO_1128ThSt_R09A.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD079777/20230911_CO_1128ThSt_R07A.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD079777/20230911_CO_1128ThSt_R10A.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD079777/search.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["thorsten.stafforst@uni-tuebingen.de"],"submitter":["Mirita Franz-Wachtel"],"technology_type":["Data-dependent acquisition","Affinity purification coupled with mass spectrometry proteomics","Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Proximity biotinylation","Rna quality control","Rna exosome","In situ biotinylation","Biotin ligase","Silac","Antisense oligonucleotide","Basu"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD079777"],"tissue":["Epithelial Cell Of Cervix"],"sample_protocol":["Proximity biotinylation experiment. Hela cells were labeled for triple SILAC using DMEM containing light (Lys0/Arg0), medium (Lys4/Arg6) and heavy (Lys8/Arg10) amino acids. Cells were treated with ADAR-recruiting oligonucleotides modified with a benzyl guanine moiety. HeLa wt cells were fixated 24 h after oligonucleotide treatment with 3.7% formaldehyde (10 min, at r.t.), conjugated with 240 nM recombinant biotin ligase (SNAP-BASU-His) and biotinylation was induced by incubation in biotinylation buffer. Lysates of three SILAC conditions were pooled (~1000 µg total) and biotinylated proteins were enriched on streptavidin magnetic sepharose. Proteins were loaded on an 8-16% Tris-Glycine Mini Gel with 1x Lämmli. The gels were stained using Coomassie Stain and destained with water. Lanes were excised; the streptavidin band was separated and measured independently. Gel pieces were digested in gel with trypsin, and desalted peptide mixtures were separated  on an Easy-nLC 1200 coupled to a Q Exactive HF mass spectrometer using a 57 minute segmented gradient of 10-33-50-90% of HPLC solvent B (80% acetonitrile in 0.1% formic acid) in HPLC solvent A (0.1% formic acid) at a flow rate of 200 nl/min. In each scan cycle, the 7 most intense precursor ions were sequentially fragmented using higher energy collisional dissociation (HCD) fragmentation. In all measurements, sequenced precursor masses were excluded from further selection for 30 s. The target values for MS/MS fragmentation were 105 charges, and for the MS scan 3×106 charges."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["MS spectra were processed with MaxQuant software package version 2.2.0.0 with integrated Andromeda search engine. Database search was performed against a target-decoy Homo sapiens database obtained from Uniprot. In addition, data were searched against the sequence of SNAP-BASU-His. In database search, full trypsin digestion specificity was required and up to two missed cleavages were allowed. Carbamidomethylation of cysteine was set as fixed modification; protein N-terminal acetylation, and oxidation of methionine were set as variable modifications. Maximum allowed mass tolerance was set to 4.5 parts per million (ppm) for precursor ions and 20 ppm for fragment ions. The amino acids Lys4/Arg6 and Lys8/Arg10 were defined as medium and heavy labels, respectively. For protein group quantitation a minimum of two quantified peptides was required. Peptide, protein and modification site identifications were reported at a false discovery rate of 0.01, estimated by the target/decoy approach."],"omics_type":["Proteomics"],"labhead":["Thorsten Stafforst"],"instrument_platform":[""],"labhead_affiliation":["Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany Gene and RNA Therapy Center (GRTC), Faculty of Medicine, University of Tübingen, Tübingen, Germany"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["Not available"],"submitter_mail":["mirita.franz@uni-tuebingen.de"],"submitter_affiliation":["Proteome Center Tuebingen"],"submitter_country":["Germany"],"additional_accession":[]},"is_claimable":false,"name":"Inhibition of the RNA exosome by chemically stabilized long antisense oligonucleotides","description":"The protein interactions of ADAR-recruiting oligonucleotides inside the cellular environment was identified using the isASO-ID protocol and SILAC-MS/MS. We identified two exoribonucleases to bind differently to the oligonucleotides with respect to their 3’-terminal 2’-ribose modifications leading to inhibition ofthe RNA exosome complex leading to accumulation of incompletely processed ribosomal RNAs and promoter upstream transcripts. This effect is dependent on the sequence, length, and 2’-ribose modifications of an 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