Individual anthocyanins and phenolic acids were quantified by HPLC as described in our previous publication.30 Briefly, filtered samples were injected (10 μL) into a 1200 HPLC system (Agilent Technologies) equipped with a UV−vis diode array detector (DAD), controlled-temperature autosampler (4°C), and column compartment (30°C) using a reversed-phase Supelcosil LC-18 column, 25 mm × 4.6 mm × 5 μm (Supelco, Bellefonte, PA, USA). Standard curves were calculated using peak areas at UV of 520 or 325 nm for anthocyanins (as cyanidin 3-O-glucoside or delphinidin 3-O-glucoside equivalents) or phenolic acids, respectively, and the known injected concentrations for the standards.
Filtered samples were injected (10 µL) into a 1200 HPLC system (Agilent Technologies, Santa Clara, CA, USA) equipped with a UV–vis diode array detector (DAD), controlled-temperature autosampler (4°C), and column compartment (30°C) using a reversed-phase Supelcosil LC-18 column, 25 mm × 4.6 mm × 5 µm (Supelco, Bellefonte, PA, USA). Standard curves were calculated using peak areas at UV of 520 nm as cyaniding-3-O-glucoside equivalents.
"],"publication":["Multi-Omics analyses reveal dynamic interactions between DNA methylation and transcriptional regulation during black raspberry ripening."],"submitter_affiliation":["NC State University"],"submitter_name":["Tzung-Fu Hsieh"],"organism_part":["fruit"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Anthocyanins and phenolic acids were extracted using 60% aqueous methanol (1% trifluoroacetic acid acid) following a previously reported method for the rapid analysis of various anthocyanins.
"],"organism":["Rubus occidentalis"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15819"],"author":["Tzung-Fu Hsieh. NC State University. thsieh3@ncsu.edu."],"data_transformation_protocol":["Peak area was determined by Agilent MassHunter Qualitative Analysis (version B.05.00) software without transformation.
"],"study_factor":["Phenotype","Genotype","Collection time point"],"submitter_email":["thsieh3@ncsu.edu"],"sample_collection_protocol":["Black raspberry NC 349, an advanced selection from a Jewell x NC 100 cross developed by Dr. James Ballington. Fruits used in this study were collected between June 10 and July 20, 2016. Black raspberry fruits at five ripening stages were collected and bio-replicates of each were collected for the metabolome experiments. Black raspberry fruit development progresses through distinct color and firmness changes, from green to red, then violet, and finally black.Please update this protocol description
"],"omics_type":["Metabolomics"],"study_design":["Metabolomics","berry","Agilent 1200 Series HPLC System","untargeted analysis","ripening","fruit","Rubus occidentalis","solvent blank"],"curator_keywords":["Metabolomics","berry","Agilent 1200 Series HPLC System","untargeted analysis","ripening","fruit","Rubus occidentalis","solvent blank"],"metabolite_name":["M578.1T5.9","cyanidin 3-rutinoside","M468.1T8.1","cyanidin 3-glucoside","M468.1T8.3","M500.3T22.6","M451.2T16","M338.1T11.3","M438.2T10.7","M590.2T10","M348.1T10.1","M348.1T7.9","cyanidin 3-sambubioside","M466.1T9.4","M431.1T6.4","M1382.7T22.6","M197.1T16.5","M690.1T15","M481.2T17.1","M428.1T8.1","M594.2T9.4","M524.3T17.8","M590.2T15.2","M688.4T22.9","M592.2T15.9","M306.1T10","M490.1T16","M364.1T5.9","M606.2T21.1","M578.1T5","M454.3T22.6","M742.2T15.4","M674.2T15","M322.1T4.8","M204.1T8.9","M398.1T16","M798.1T7.5","M1016.2T14.9","M697.4T22.6","M131.1T4.5","M131.1T4.8","M958.1T7.5","M866.2T4.8","M562.1T6.1","peonidin 3-rutinoside","M398.1T16.5","M636.2T16.9","M534.1T19.4","cyanidin 3-xylosylrutinoside","M744.2T8.6","pelargonidin 3-rutinoside","M391.1T4.9","M350.1T7.7","M364.1T15","pelargonidin 3-glucoside","M578.1T6.7","M596.2T10.4","M438.1T9.6","M610.2T18.1","M448.2T16.7","M358.1T4.8","M290.1T6.4","M678.3T21.1","M518.3T22.6","M165.1T6.3","M299.1T5.8","M686.4T23.6","M464.1T18.1","M594.2T18.7","M965.1T3.8","M608.2T22.1","M492.1T17.2","M478.1T17.8","M612.2T9.4","M674.4T22.3","M348.1T15","M228T4.2","M266.1T8.1","M354.1T5","M968.1T7.5","M187.1T8.9","M528.2T19.5","M354.1T8","M702.4T22.6","M866.2T5.6","M290.1T10.1","M562.1T7.3","M914.3T8.1","M468.2T23.7"],"additional_accession":[]},"is_claimable":false,"name":"Multi-Omics analyses reveal dynamic interactions between DNA methylation and transcriptional regulation during black raspberry ripening","description":"We show developmental-series transcriptome, methylome, and metabolome to reveal extensive epigenetic reprogramming during black raspberry (Rubus occidentalis) fruit ripening. Multi-omics integration reveals coordinated anthocyanin accumulation parallels expression of biosynthetic and regulatory genes within coherent networks. Our study highlights both genome-wide and locus-specific epigenetic reprogramming and demonstrates a coordinated interplay between DNA methylation and transcriptional regulation during black raspberry fruit ripening.","dates":{"publication":"2026-09-28","submission":"2026-09-27"},"accession":"MTBLS15819","cross_references":{"KEGG":["C7 H11 N O3","C9 H19 N O","C7 H9 N4 O2","C14 H25 N O4","Cinnamic acid bornyl ester","Clusifoliol","C22 H43 N O","C12 H12 N3 O13","C17 H19 N8 O6","C22 H27 N8 O3","Catechin-4-ol 3-O-beta-D-glycopyranoside nullnullnull 8.068","Catechin-4-ol 3-O-beta-D-glycopyranoside","C22 H36 N8 O4","C25 H31 N5 O5","Coussaric acid","C20 H10 N7 O9","Cucurbitacin F","C22 H12 N7 O10","C34 H68 N2 O2","C30 H50 N18","C38 H68 N3 O7","C36 H54 N3 O10","C35 H46 N10 O6","C40 H60 N3 O10","C29 H22 N21 O5"]}}