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Following sorting, plates were centrifuged at 150 × g for 2 minutes.At 24 hours post-sorting, 150 μL of somitoid medium without ROCK inhibitor was added to each well. The medium was subsequently refreshed with NDiff227 at 48 and 72 hours. At 96 hours, medium was replaced with NDiff227 or NDiff227 supplemented with 10% Matrigel (Corning, 356231). Time course analyses were carried out using two or three independent biological replicates. Each biological replicate consists of 96 aggregates at the 48h time point and 48 somitoid structures at the 72h, 96h and 120h timepoints. iPSCs and somitoids were washed with PBS and collected by centrifugation. Pellets were resuspended in lysis buffer (150 mM NaCl, 50 mM Tris pH 8.0, 1 mM EDTA, 10% glycerol, 1% NP-40, 1 mM DTT, and complete protease inhibitors (CPI)) and sonicated (5 cycles, 30 on, 30 off) with a Bioruptor Pico (Diagenode). Protein concentration was determined with a BCA protein assay, and 20 μg of protein for each replicate was used whenever sufficient material was available.  Prior to SP3 method, protein was precipitated with acetone and pellets were dissolved in a Urea buffer (8M urea, 100 mM Tris-HCl pH 8.0, 10 mM DTT) followed by shaking at room temperature for 30 minutes. Following, iodoacetamide was added at a final concentration of 50 mM and incubated for 20 minutes at room temperature. For SP3 method, Sera-Mag™ SpeedBeads (Sigma, GE65152105050250) and Sera-Mag™ Carboxylate-Modified Magnetic Particles (Sigma, GE45152105050250) were mixed in a 1:1 ratio. Prewashed SP3 beads were added to the lysate, followed by the addition of 1.4 volumes of acetonitrile, and incubated at room temperature for 20 minutes. Beads were immobilized using a magnetic rack and washed twice with 70% ethanol and once with acetonitrile (Biosolve, 1204101BS). After air-drying, beads were resuspended in 50 uL of 50 mM ABC and supplemented with 0.1 μg trypsin (Promega, V5280). Proteins were digested for two hours while shaking at 37°C, after which the supernatants were collected. Another 50 μL of ABC (50 mM) was added to the beads, incubated for 5 minutes in a thermoshaker and supernatants were combined with the first elution. Digestion was then continued overnight at 37°C. The following day, peptides were acidified by adding 10 μL of 10% v/v TFA (Biosolve, 202341) and subsequently purified on C18 Stagetips. Digested peptides were eluted from homemade C18 StageTips using buffer B (0.1% formic acid, 80% acetonitrile) and reconstituted in buffer A (0.1% formic acid) to a final volume of 40 μL for SP3 samples and 12 μL for pulldown samples. Eluted peptides were loaded onto a Vanquish Neo nano-LC system (Thermo Scientific) coupled to an Orbitrap Astral mass spectrometer (Thermo Scientific) operating in data-independent acquisition (DIA) mode. Peptides were separated on a 25 cm column (IonOpticks , AUR3-25075C18XT) using a 42- minute active gradient with a flow rate 400 nL/min increasing to 500 nL/min during the wash out. MS1 scans were acquired from 380 to 980 m/z at 240,000 resolution. RF lens (%) was set to 40 and the normalized AGC target was set to 500% with a maximum injection time of 5ms. For DIA MS2, a normalized HCD collision energy of 25% was applied to a 380-980 m/z precursor range using non-overlapping isolation windows of 2Th, with window placement optimization turned on. Scans were acquired in the Astral analyzer over a 150-2000 m/z range, with the normalized AGC target set to 500% with a maximum injection time of 3 ms."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Raw mass spectrometry spectra were processed using DIA-NN software (version 1.9.2) (Demichev et al., 2020) with the library-free search method and match between runs enabled. We used a FASTA file of the Homo sapiens proteome, downloaded from UniProt in June 2024 (UniProtKB proteome ID: UP000005640). Additionally, a FASTA file containing common contaminants from the cRAP database (April 2019 release) was included as a contaminant list. Trypsin was specified as the proteolytic enzyme, allowing for up to two missed cleavages. Cysteine carbamidomethylation, methionine oxidation, N-terminal methionine excision, and N-terminal acetylation were included as modifications, with a maximum of five variable modifications per peptide. Protein groups with more than two unique peptides and quantified in all replicates of at least one experimental group were retained for downstream analysis. For time course analyses, data normalization was performed using variance stabilizing normalization (VSN) within the DEP R package. Missing values were imputed by sampling from a left shifted Gaussian distribution relative to the observed data distribution. Data visualization was performed using ggplot2 in R (version 4.4.1)."],"omics_type":["Proteomics"],"labhead":["Suzan Stelloo"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Department of Urology, Radboud Institute for Medical Innovation, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA, Nijmegen, The Netherlands."],"species":["Homo Sapiens (human)"],"publication":["42561940 Alejo-Vinogradova MT,Strøm YE,Lamers LA,Chang YW,Hendriksen MJ,Moosajee M,Vermeulen M,Stelloo S From stem cells to somites: Revealing genetic and exogenous factors of human embryogenesis. Stem Cell Reports. 2026 Aug 6:103023 10.1016/j.stemcr.2026.103023"],"submitter_mail":["stelloo@science.ru.nl"],"submitter_affiliation":["Department of Urology, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands"],"submitter_country":["Netherlands"],"additional_accession":[]},"is_claimable":false,"name":"From stem cells to somites: revealing genetic and exogenous factors of human embryogenesis","description":"In this project, we characterized the temporal dynamics of protein expression during the differentiation of human iPSCs to somitoids, stem cell–derived 3D models that recapitulate early embryonic somitogenesis. Using quantitative time-course proteomics, we captured how protein abundance changed as pluripotent stem cells progressed into segmented, organized structures, providing insight into the molecular processes underlying human axial development.","dates":{"publication":"2026-08-07","submission":"2026-06-01"},"accession":"PXD079129","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","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:111205","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:10034","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:1589","NEWT:135622","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:383379","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:641809","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: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: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:1182590","NEWT:3712","NEWT:3711","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:244366","NEWT:1246791","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","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:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2853422","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:95486","NEWT:1883446","NEWT:1233435","NEWT:109760","NEWT:29031","NEWT:235443","NEWT:1757312","NEWT:85694","NEWT:108458","NEWT:5936","NEWT:320637","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:472","NEWT:940825","NEWT:529507","NEWT:1071661","NEWT:470","NEWT:5911","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:9031","NEWT:27292","NEWT:1050722","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:51338","NEWT:575412","NEWT:28112","NEWT:6493","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:8655","NEWT:5147","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:443906","NEWT:519","NEWT:2510939","NEWT:7394","NEWT:6063","NEWT:1328388","NEWT:1548728","NEWT:667127","NEWT:9557","NEWT:377586","NEWT:300641","NEWT:39655","NEWT:9554","NEWT:38323","NEWT:256318","NEWT:206411","NCBITaxon:6191","NEWT:229533","NEWT:214053","NEWT:80863","NEWT:90675","NEWT:52638","NEWT:57075","NEWT:1666905","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:1123869","NEWT:9544","NEWT:9545","NEWT:979","NEWT:7370","NEWT:83906","NEWT:1134506","NEWT:255470","NEWT:38783","NEWT:6426","NEWT:33090","NEWT:9935","NEWT:287889","NEWT:305959","NEWT:13489","NEWT:92867","NEWT:92866","NCBITaxon:3055","NEWT:51750","NEWT:202950","NEWT:295027","NCBITaxon:11320","NEWT:632957","NEWT:9925","NCBITaxon:9606","NEWT:90690","NEWT:1436183","NEWT:4232","NEWT:416348","NEWT:11298","NEWT:4236","NEWT:7742","NEWT:196627","NEWT:200308","NEWT:200302","NEWT:870435","NEWT:9913","NEWT:9915","NEWT:105841","NEWT:2666255","NEWT:999810","NCBITaxon:5693","NEWT:28995","NEWT:1392998","NEWT:380394","NEWT:226900","NEWT:1266738","NEWT:231490","NEWT:244704","NEWT:7725","NEWT:9909","NEWT:9902","NEWT:430615","NEWT:563041","NEWT:72664","NEWT:36599","NEWT:41949","NEWT:326423","NEWT:452467","NEWT:198822","NEWT:36111","NEWT:32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