{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/P2960_fractionated_ion.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/P2960_fractionated_protein.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/P2960_fractionated_peptide.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/P2960_fractionated_psm.tsv"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/annotation.txt"],"Csv":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/metadata.csv"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/Zelda_231117_P2960_PH_FC_TMT12_R1_F10.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/Zelda_231117_P2960_PH_FC_TMT12_R1_F12.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/Zelda_231117_P2960_PH_FC_TMT12_R1_F01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/Zelda_231117_P2960_PH_FC_TMT12_R1_F06.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/Zelda_231117_P2960_PH_FC_TMT12_R1_F04.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/Zelda_231117_P2960_PH_FC_TMT12_R1_F11.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/Zelda_231117_P2960_PH_FC_TMT12_R1_F02.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/Zelda_231117_P2960_PH_FC_TMT12_R1_F07.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/Zelda_231117_P2960_PH_FC_TMT12_R1_F05.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/Zelda_231117_P2960_PH_FC_TMT12_R1_F08.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/Zelda_231117_P2960_PH_FC_TMT12_R1_F03.raw"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/UP000000589_MusMusculus_C57BL_ID10090_21968entries_27102022_dl11012023.fasta"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053069/FragPipe_workflow.workflow"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["Rory.Morty@med.uni-heidelberg.de"],"submitter":["Frank Stein"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"software":[""],"submitter_keywords":["Microrna","Development","In vivo mimic"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD053069"],"tissue":["Lung","Liver"],"sample_protocol":["Lung and liver samples from newborn mice were perfused with PBS 1x and any adjacent tissue was carefully removed. Samples were homogenized in polypropylene tubes with screw cap containing 300 μl of SDS 2%, 10% COMPLETE® protease inhibitor and metallic beads at 300 Hz for 3 minutes. The homogenized content was transferred to 1.5 ml Eppendorf® tubes and centrifuged at 12.000g for 10 minutes. Protein concentration in the resulting supernatant was measured  with tryptophan assay and 50 μg of protein from each sample was submitted for proteomic analysis.For the mass spectrometric analysis, lysates containing 10 µg of protein were subjected to an in-solution tryptic digest, following a modified version of the Single-Pot Solid-Phase-enhanced Sample Preparation (SP3) technology (PMID: 25358341, PMID: 29565595). 20 µl of a slurry of hydrophilic and hydrophobic Sera-Mag Beads (Thermo Scientific, #4515-2105-050250, 6515-2105-050250) were mixed, washed with water and were then reconstituted in 100 µl water. 5 µl of the prepared bead slurry were added to 50 µl of the eluate following the addition of 55 µl of acetonitrile. All further steps were prepared using the King Fisher Apex System (Thermo Scientific). After binding to beads, beads were washed three times with 100 µl of 80% ethanol before they were transferred to 100 µl of digestion buffer (50 mM Hepes/NaOH pH 8.4 supplemented with 5 mM TCEP, 20 mM chloroacetamide (Sigma-Aldrich, #C0267), and 0.25 µg trypsin (Promega, #V5111)). Samples were digested over night at 37°C, beads were removed and the remaining peptides were dried down.Peptides were reconstituted in 10 µl of H2O and reacted for 1 h at room temperature with 80 µg of TMT10plex (Thermo Scientific, #90111) or TMTpro (Thermo Scientific, #A44522) label reagent dissolved in 4 µl of acetonitrile. Excess TMT reagent was quenched by the addition of 4 µl of an aqueous 5% hydroxylamine solution (Sigma, 438227). Peptides were reconstituted in 0.1 % formic acid, mixed to achieve a 1:1 ratio across all TMT-channels and purified by a reverse phase clean-up step (OASIS HLB 96-well µElution Plate, Waters #186001828BA).Peptides were subjected to an offline fractionation under high pH conditions (PMID: 25358341). The resulting 12 fractions were then analyzed by LC-MS/MS on an Orbitrap Fusion Lumos mass spectrometer (Thermo Scentific) as previously described (PMID:30858367).To this end, peptides were separated using an Ultimate 3000 nano RSLC system (Dionex) equipped with a trapping cartridge (Precolumn C18 PepMap100, 5 mm, 300 μm i.d., 5 μm, 100 Å) and an analytical column (Acclaim PepMap 100. 75 × 50 cm C18, 3 mm, 100 Å) connected to a nanospray-Flex ion source. The peptides were loaded onto the trap column at 30 µl per min using solvent A (0.1% formic acid) and eluted using a gradient from 2 to 80% Solvent B (0.1% formic acid in acetonitrile) over 2 h at 0.3 µl per min (all solvents were of LC-MS grade). The Orbitrap Fusion Lumos was operated in positive ion mode with a spray voltage of 2.4 kV (TMT10plex) or 2.2 kV (TMTpro) and capillary temperature of 275 °C. Full scan MS spectra with a mass range of 375–1500 m/z were acquired in profile mode using a resolution of 120,000 (maximum fill time of 50 ms or a maximum of 4e5 ions (AGC) and a RF lens setting of 30%. Fragmentation was triggered for 3 s cycle time for peptide like features with charge states of 2–7 on the MS scan (data-dependent acquisition). Precursors were isolated using the quadrupole with a window of 0.7 m/z and fragmented with a normalized collision energy of 38% (TMT10plex) or 34% (TMTpro). Fragment mass spectra were acquired in profile mode and a resolution of 30,000 in profile mode. Maximum fill time was set to 64 ms or an AGC target of 1e5 ions for TMT10plex. For TMTpro the maximum injection time was set to 94 ms and the AGC target was set to custom. The dynamic exclusion was set to 45 s (TMT10) or to 60 s (TMTpro)."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Acquired data were analyzed using FragPipe (PMID: 28394336) and a Uniprot Mus musculus fasts database (UP000000589, ID10090 with 21.968 entries, date: 27.10.2022, downloaded: January 11th 2023) including common contaminants. The following modifications were considered: Carbamidomethyl (C, fixed), TMT10 or TMT16plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10 or TMT16plex (N-term, variable). The mass error tolerance for full scan MS spectra was set to 10 ppm and for MS/MS spectra to 0.02 Da. A maximum of 2 missed cleavages were allowed. A minimum of 2 unique peptides with a peptide length of at least seven amino acids and a false discovery rate below 0.01 were required on the peptide and protein level (PMID: 25987413).The raw output files of FragPipe (protein.tsv files) were processed using the R programming language (ISBN 3-900051-07-0). Contaminants and reverse proteins were filtered out and only proteins that were quantified with at least 2 razor peptides (Razor.Peptides >= 2) were considered for the analysis. 5956 proteins passed the quality control filters. Log2 transformed raw TMT reporter ion intensities ('channel' columns) were first cleaned for batch effects using the 'removeBatchEffect' function of the limma package (PMID: 25605792) and further normalized using the 'normalizeVSN' function of the limma package (VSN - variance stabilization normalization - PMID: 12169536). Proteins were tested for differential expression using a moderated t-test by applying the limma package ('lmFit' and 'eBayes' functions). The replicate information was added as a factor in the design matrix given as an argument to the 'lmFit' function of limma. The t-value output of limma for certain statistical comparisons was analyzed with the 'fdrtool' function of the fdrtool packages (PMID: 18441000) in order to extract p-values and false discovery rates (q-values were used). A protein was annotated as a hit with a false discovery rate (fdr) smaller 0.05 and an absolute fold-change of greater 2 and as a candidate with a fdr below 0.2 and an absolute fold-change of at least 1.5."],"omics_type":["Proteomics"],"labhead":["Rory Morty"],"instrument_platform":[""],"labhead_affiliation":["Heidelberg University Hospital"],"submission_type":["PARTIAL"],"species":["Mus Musculus (mouse)"],"submitter_mail":["frank.stein@embl.de"],"publication":["42498504 Willen S, Myti D, Obeidat R, Casado F, Khaghani Raziabad S, Nardiello C, Günther S, Haberkant P, Stein F, Khan MM, Pepperkok R, Rickert-Zacharias V, Vadász I, Herold S, Hilgendorff A, Mižik I, Seeger W, Morty RE. Functional delivery of commercially-available microRNA mimics to the organs of developing mice. RNA. 2026:rna.081174.126 10.1261/rna.081174.126"],"submitter_affiliation":["EMBL"],"submitter_country":["Germany"],"pubmed_abstract":["MicroRNA are pivotal regulators of organ and tissue homeostasis and development, and pathogenic mediators of disease. While antagonism of specific microRNA species <i>in vivo</i> is easily accomplished in experimental animal models using locked nucleic acid (LNA)-stabilized antimiRs, microRNA mimicry -that is, increasing the abundance of specific microRNA species- in experimental animals is more challenging. In this study, commercially available naked LNA-stabilized oligonucleotides designed as microRNA mimics were assessed for efficacy in newborn mouse pups, which frequently serve as models for normal human development, or neonatal and pediatric disease. Mimics targeting miR-497a-5p commercially marketed for <i>in vivo</i> or <i>in vitro</i> use were examined for distribution to five organs in developing mouse pups after parenteral administration. Mimics were most effectively delivered to the liver, and in limited instances also to the heart and kidneys, but could not be detected in the brain or lungs. A combination of bulk RNA-Seq transcriptomic screening and proteomic screening of liver homogenates revealed that mimics delivered to the liver were functional, either reducing the abundance of the <i>Tff3</i> mRNA transcript, or the abundance of N4bp1 or Mt2 proteins, all of which are cognate targets of miR 497a-5p. Furthermore, the data presented here demonstrate that LNA-stabilized mimics for miR-497a-5p were short-lived <i>in vivo</i>, yet impacted the abundance of both primary and secondary targets of miR-497a-5p albeit with demonstrable hepatotoxicity. This study concludes that while microRNA mimicry using commercially-available naked LNA stabilized oligonucleotides is possible, there remains tremendous scope -and need- for refinement of this technology."],"pubmed_title":["Functional delivery of commercially-available microRNA mimics to the organs of developing mice."],"pubmed_authors":["Willen Sven S, Myti Despoina D, Obeidat Razan R, Casado Francisco F, Khaghani Raziabad Solmaz S, Nardiello Claudio C, Günther Stefan S, Haberkant Per P, Stein Frank F, Khan Muzamil M MM, Pepperkok Rainer R, Rickert-Zacharias Verena V, Vadász István I, Herold Susanne S, Hilgendorff Anne A, Mižik Ivana I, Seeger Werner W, Morty Rory E RE"],"additional_accession":[]},"is_claimable":false,"name":"Mimic miR-497a-5p in vivo intervention","description":"The use of microRNA mimics to increase microRNA levels in the developing organs of newborn  mice.  Livers from mice treated with 100 mg/kg of an in vivo miR-497a-5p LNA mimic at postnatal day (P)1 and P3 were harvested at postnatal day (P)5.  Lungs and livers from mice treated with daily 10 mg/kg intraperitoneal injections of an in vivo miR-497a-5p mimic were harvested at postnatal day 14.","dates":{"publication":"2026-07-13","submission":"2024-06-13"},"accession":"PXD053069","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NEWT:625351","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:6819","NEWT:475174","NEWT:111205","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:10034","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:1589","NEWT:135622","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:1582","NEWT:36630","NEWT:383379","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:1392488","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:111225","NEWT:7719","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:3347","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:410658","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:44685","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:150808","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:3714","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:28174","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:3704","NEWT:244366","NEWT:1246791","NEWT:176597","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:33995","NEWT:55784","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2499525","NEWT:2853422","NEWT:487","NEWT:1538553","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:237610","NEWT:95486","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:11757","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:491","NEWT:460523","NEWT:45954","NEWT:235443","NEWT:1757312","NEWT:85694","NEWT:109786","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:373153","NEWT:1640278","NEWT:472","NEWT:940825","NEWT:529507","NEWT:1071661","NEWT:28128","NEWT:470","NEWT:5911","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:906914","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:3728","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:207340","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:771870","NEWT:51338","NEWT:575412","NEWT:28112","NEWT:6493","NEWT:10832","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:5147","NEWT:28108","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:1613","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:298176","NEWT:353153","NEWT:227377","NEWT:1774284","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:443906","NEWT:519","NEWT:2510939","NEWT:7394","NEWT:6063","NEWT:1328388","NEWT:105487","NEWT:1548728","NEWT:667127","NEWT:9557","NEWT:377586","NEWT:300641","NEWT:39655","NEWT:9554","NEWT:38323","NEWT:475932","NEWT:256318","NEWT:206411","NCBITaxon:6191","NEWT:229533","NEWT:214053","NEWT:28550","NEWT:80863","NEWT:90675","NEWT:52639","NEWT:52638","NEWT:57075","NEWT:1666905","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:510516","NEWT:1045775","NEWT:1123869","NEWT:9544","NEWT:9545","NEWT:979","NEWT:7370","NEWT:83906","NEWT:99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