Summary of Study ST003843

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002401. The data can be accessed directly via it's Project DOI: 10.21228/M88V68 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST003843
Study TitleMetabolomics Analysis of the Silkworm Cocoon Shell
Study Typemetabolomics
Study SummaryIn this study we conducted metabolomics analyses of historical and contemporary Bombyx mori cocoon shells to case-study the human-driven introduction and diversification of this species in Europe. We employed LC-MS/MS analyses protocols for 80 cocoon shell samples to identify that the cocoon shell of this species contains 141 metabolites in 80% of the samples. Our metabolomics datasets provide a valuable foundation for advancing further exploitations of silkworm cocoon shells in multiple scientific perspectives.
Institute
National and Kapodistrian University of Athens
DepartmentBiology
LaboratoryZoology
Last NameDedos
First NameSkarlatos
AddressPanepistimioupoli Zografou, Athens, Attiki, 15784, Greece
Emailsdedos@biol.uoa.gr
Phone0030-2107274705
Submit Date2025-03-28
Num Groups1
Total Subjects80
PublicationsPending
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-07-15
Release Version1
Skarlatos Dedos Skarlatos Dedos
https://dx.doi.org/10.21228/M88V68
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002401
Project DOI:doi: 10.21228/M88V68
Project Title:Multiomics Coalescent Analyses Delineates the Complex Anthropogenic Evolution of Silkworm Races in Europe
Project Type:Metabolomics and Lipidomics
Project Summary:Employing phenomics, proteomics, metabolomics and lipidomics, this study identifies the introduction routes and anthropogenic evolution of European silkworm races, a clade of silkworm races with unresolved and obscure ancestry. Prompted by recent findings on the genomic variability that underlies the ancestry and cocoon shell colour of the silkworm, Bombyx mori, we carried out a large-scale analysis of historical and contemporary cocoon shells of this species. By taking our datasets through a series of dimensionality reduction and clustering algorithms, in conjunction with narratives from historical archives that attest to continuous familial interbreeding and constant influx of silkworm races in Europe, we identify three regional hotspots of diversification of these European silkworm races. Furthermore, and in agreement with recent genomic analyses which show an early evolutionary divergence of European silkworm races, we show that these races exhibit human-driven phenotypic innovations, during their domestication in Europe, caused by continuous familial breeding, selection for a limited number of traits and limited regional segregation. Our multiomics datasets provide a valuable foundation for advancing further exploitations of silkworm cocoon shells and show that the European silkworm races are lineages of races that evolved in Central Asia and the Middle East before arriving in Europe and then continuously interbred and improved through introduction of Chinese and Japanese silkworm races.
Institute:National and Kapodistrian University of Athens
Department:Biology
Laboratory:Zoology
Last Name:Dedos
First Name:Skarlatos
Address:Panepistimioupoli Zografou, Athens, Attiki, 15784, Greece
Email:sdedos@biol.uoa.gr
Phone:0030-2107274705
Funding Source:This research was founded by the project: Advocating the Role of silk Art and Cultural heritage at National and European scale - Aracne (European Union’s Horizon Europe Research and Innovation Programme: Grant Agreement No 101095188).
Project Comments:This is a study of 80 Bombyx mori cocoon shell samples analysed for their metabolites and lipids content
Publications:Pending
Contributors:Panagiota Fragkoua, Ioannis Martakosb, Georgia Rounic, Demetrios Vasilakosa, Evangelos Koutsoukosa, Alesssio Savianed, Silvia Cappellozzad, Marios G. Kostakisb, Martina Samiotakic, Sotiris Kotsiantise, Mariana Barcenasf**, Skarlatos G. Dedosa*

Subject:

Subject ID:SU003977
Subject Type:Insect
Subject Species:Bombyx mori
Taxonomy ID:7091

Factors:

Subject type: Insect; Subject species: Bombyx mori (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Region Sample_type
SA420387QC_01Blank Internal Standard Quality Control
SA420388QC_03Blank Internal Standard Quality Control
SA420389QC_04Blank Internal Standard Quality Control
SA420390QC_05Blank Internal Standard Quality Control
SA420391QC_06Blank Internal Standard Quality Control
SA420392QC_07Blank Internal Standard Quality Control
SA420393QC_08Blank Internal Standard Quality Control
SA420394QC_09Blank Internal Standard Quality Control
SA420395QC_10Blank Internal Standard Quality Control
SA420396QC_11Blank Internal Standard Quality Control
SA420397QC_12Blank Internal Standard Quality Control
SA420398QC_13Blank Internal Standard Quality Control
SA420399QC_14Blank Internal Standard Quality Control
SA420400QC_15Blank Internal Standard Quality Control
SA420401QC_16Blank Internal Standard Quality Control
SA420402QC_17Blank Internal Standard Quality Control
SA420403QC_18Blank Internal Standard Quality Control
SA420404QC_19Blank Internal Standard Quality Control
SA420405QC_20Blank Internal Standard Quality Control
SA420406QC_02Blank Internal Standard Quality Control
SA42040735_47_Erevan (Armenia)Cocoon shell Armenia Old
SA42040838_50_Shanghai 1881Cocoon shell China Old
SA42040927_39_SuzhouCocoon shell China Old
SA42041029_41_Bombyx textor (China)Cocoon shell China Old
SA42041180_139_European-No16-oldCocoon shell Europe New
SA42041279_138_Yu?hakuCocoon shell Europe New
SA42041372_123_Kokuga (Black moth)Cocoon shell Europe New
SA42041471_122_Kinto (Golden pink)Cocoon shell Europe New
SA42041567_116_BagdadCocoon shell Europe New
SA42041651_65_p31Cocoon shell Europe New
SA4204175_7_BagdadCocoon shell Europe Old
SA42041876_131_St Julien? (Sanjurian)Cocoon shell France New
SA42041970_121_GubbioCocoon shell France New
SA42042069_119_Blanc des CevennesCocoon shell France New
SA42042148_61_Var FranceCocoon shell France Old
SA4204227_11_Sevenien WhiteCocoon shell France Old
SA42042310_15_French WhiteCocoon shell France Old
SA42042455_80_FranceCocoon shell France Old
SA42042513_18_Vari YellowCocoon shell France Old
SA4204264_6_Corsican YellowCocoon shell France Old
SA42042743_55_Corsica FranceCocoon shell France Old
SA4204283_5_Alpine YellowCocoon shell France Old
SA4204291_3_Kakhuri GreenCocoon shell Georgia New
SA42043011_16_Tetrparkiani ie GeorgianCocoon shell Georgia New
SA42043136_48_Tiflis (Georgia)Cocoon shell Georgia Old
SA42043234_46_Schwatzwald (Germany)Cocoon shell Germany Old
SA42043330_42_MakedoniaCocoon shell Greece Old
SA42043464_109_KomotiniCocoon shell Greece Old
SA42043577_132_SzegsardCocoon shell Hungary New
SA42043654_78_Nistri (India)Cocoon shell India Old
SA42043728_40_Bombyx croesi (India)Cocoon shell India Old
SA42043850_63_Dehra Dun IndiaCocoon shell India Old
SA42043966_112_KashmereCocoon shell India Old
SA42044032_44_IranCocoon shell Iran Old
SA42044137_49_Iran (yellow)Cocoon shell Iran Old
SA42044249_62_Bagdad IraqCocoon shell Iraq Old
SA42044378_136_y35(Gran Sasso)Cocoon shell Italy New
SA42044474_128_RosaCocoon shell Italy New
SA42044568_118_BioneCocoon shell Italy New
SA42044673_124_Maiella-ZebraCocoon shell Italy New
SA42044762_103_APCocoon shell Italy New
SA42044861_101_HAN HANCocoon shell Italy New
SA42044960_99_TREOTTO ROSACocoon shell Italy New
SA42045059_98_PVNCocoon shell Italy New
SA42045163_104_ASCOLICocoon shell Italy New
SA42045258_95_VM2ACocoon shell Italy New
SA42045365_110_Bianco ItaliaCocoon shell Italy Old
SA42045419_27_Sample No 5Cocoon shell Italy Old
SA42045523_35_Sample No 13Cocoon shell Italy Old
SA42045622_33_Sample No 11Cocoon shell Italy Old
SA42045721_31_Sample No 9Cocoon shell Italy Old
SA42045820_29_Sample No 7Cocoon shell Italy Old
SA42045916_23_Sample No 1Cocoon shell Italy Old
SA42046018_26_Sample No 4Cocoon shell Italy Old
SA42046117_24_Sample No 2Cocoon shell Italy Old
SA42046215_22_Gran-SassoCocoon shell Italy Old
SA42046314_20_Italian YellowCocoon shell Italy Old
SA42046412_17_Italian GreenCocoon shell Italy Old
SA42046524_36_Sample No 14Cocoon shell Italy Old
SA42046645_57_Bione ItalyCocoon shell Italy Old
SA4204678_12_Italian WhiteCocoon shell Italy Old
SA42046831_43_Cosenza (Italy)Cocoon shell Italy Old
SA42046953_70_c42Cocoon shell Japan New
SA42047052_69_c44Cocoon shell Japan New
SA42047156_81_Shirahine (Shirohime) (Japan)Cocoon shell Japan Old
SA42047247_60_KoreaCocoon shell Korea Old
SA42047344_56_Ryazan RussiaCocoon shell Russia Old
SA42047440_52_Galati RomaniaCocoon shell Russia Old
SA42047575_130_SpainCocoon shell Spain New
SA4204769_14_Iberian Peninsula YellowCocoon shell Spain Old
SA42047725_37_Espaniola 1910Cocoon shell Spain Old
SA42047826_38_Pacheco del Pais 1910Cocoon shell Spain Old
SA42047941_53_Murcua SpainCocoon shell Spain Old
SA4204806_8_Iberian Peninsula YellowCocoon shell Spain Old
SA42048157_82_Almeria (Spain)Cocoon shell Spain Old
SA42048242_54_SwitzerlandCocoon shell Switzerland Old
SA42048346_59_ThailandCocoon shell Thailand Old
SA4204842_4_Bursa?s WhiteCocoon shell Turkey Old
SA42048539_51_Bursa TurkeyCocoon shell Turkey Old
SA42048633_45_UzbekistanCocoon shell Uzbekistan Old
Showing results 1 to 100 of 100

Collection:

Collection ID:CO003970
Collection Summary:A set of 80 of the 148 cocoon shell samples were selected for metabolomics and lipidomics analysis. The set of the 80 selected samples is shown in Supplementary File s1. A pilot study was carried out with 4 additional samples to validate every step of the sample analysis and assess its feasibility. The results of the pilot study are not included in the analysis of the 80 samples. A careful selection of the 80 cocoon shell samples was carried out aiming to avoid as much as possible ambiguously-labelled B. mori mutants (see Supplementary File s1) as well as samples with known parental-sibling relationships (i.e. samples 141-147, see Supplementary File s1) that would skew the analysis results. Purposefully, samples of the same name or similar geographic location were used in the analysis to assess the effect of the place of origin and sample freshness on the obtained results.
Collection Protocol Filename:Materials_and_Methods_Metabolomics.pdf
Sample Type:Cocoon shells
Collection Method:Museum and geneticl resources centers
Collection Location:Europe
Collection Frequency:Not applicable
Collection Duration:12 Months
Volumeoramount Collected:80 samples
Storage Conditions:Room temperature
Collection Vials:80
Storage Vials:80
Collection Tube Temp:RT

Treatment:

Treatment ID:TR003986
Treatment Summary:No treatment to the old or contemporary cocoon shell samples

Sample Preparation:

Sampleprep ID:SP003983
Sampleprep Summary:For biphasic extraction of lipids and polar metabolites, cocoons were cut into small pieces and placed in 5 mL centrifuge tubes. Three (3) mL of MeOH (containing internal standards) were initially added to the cocoon samples. After vortexing and ultrasonic bath extraction for 10 min, 1.8 mL of supernatant were collected and transferred to clean 15 mL centrifuge tubes. Subsequently, 4.5 mL of MTBE were added and the monophasic mixture was vortexed for 60 s and incubated at -20 °C for 20 min. For phase separation, 1.2 mL water were added, followed by another vortexing and incubation step (see previous conditions). The biphasic solvent system was then centrifuged for 15 min at 5000 rpm and 4 °C with a 5810R centrifuge (Eppendorf, Germany). For lipidomics analysis, 4 mL of the upper organic phase were transferred, dried under a stream of nitrogen, and reconstituted in 100 µL IPA:MeOH (50:50, v/v). For metabolomics analysis, 2.4 mL of the lower aqueous phase were transferred, dried under a stream of nitrogen, and reconstituted in 75 µL 80% MeOH (v/v). The final samples were vortexed for 10 min, centrifuged (see previous conditions) and the supernatants were transferred to analytical glass vials for LC-MS/MS analysis.
Sampleprep Protocol Filename:Materials_and_Methods_Metabolomics.pdf
Processing Storage Conditions:Described in summary
Extraction Method:Described in summary
Sample Resuspension:Described in summary
Sample Derivatization:Described in summary
Sample Spiking:Described in summary
Subcellular Location:Not applicable

Chromatography:

Chromatography ID:CH004793
Chromatography Summary:See Materials_and_Methods_Metabolomics.pdf
Methods Filename:Materials_and_Methods_Metabolomics.pdf
Instrument Name:Thermo Vanquish
Column Name:Waters Atlantis Premier BEH Z-HILIC (100 x 2.1mm, 1.7um)
Column Temperature:40°C
Flow Gradient:20 min total run time including re-equilibration was applied (time [min]/%B): 0/95, 2/95, 14.5/60, 16/60, 16.5/95, 20/95
Flow Rate:0.25 mL/min
Solvent A:90% water/10% acetonitrile
Solvent B:90% acetonitrile/10% water
Chromatography Type:HILIC

Analysis:

Analysis ID:AN006316
Laboratory Name:Metabolomics Core Facility, EMBL Heidelberg
Analysis Type:MS
Analysis Protocol File:Materials_and_Methods_Metabolomics.pdf
Chromatography ID:CH004793
Num Factors:27
Num Metabolites:115
Units:Signal Intensity
  
Analysis ID:AN006317
Laboratory Name:Metabolomics Core Facility, EMBL Heidelberg
Analysis Type:MS
Analysis Protocol File:Materials_and_Methods_Metabolomics.pdf
Chromatography ID:CH004793
Num Factors:27
Num Metabolites:89
Units:Signal Intensity
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