← All .science files
pmid:27331114
Data on the kinetics of in vitro assembled chromatin.
Moritz Carl Völker-Albert · Miriam Caroline Pusch · Andreas Schmidt · Axel Imhof
Data in brief · 2016 doi:10.1016/j.dib.2016.05.057
Paper
complete
Experiment
partial
Data
partial
Analysis
partial
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 4 items
claims array · 3 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[1] object · 6 fields
[2] object · 6 fields
evidence array · 4 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[3] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 1 item
data object · 3 fields
assets array · 1 item
[0] object · 15 fields
structure object · 4 fields
gaps array · 0 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
targets array · 0 items
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 0 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 0 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 1 item
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 1 item
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 6 items
assays array · 1 item
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27331114", "kind": "science-record", "revision": 6, "content_hash": "sha256:dd7ce799af64e6a6c107a5347e8f64a05aedb8e372205de531ed8b0c7d8699b0", "created_at": "2026-11-01T15:40:18Z", "updated_at": "2026-11-01T21:20:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Data on the kinetics of in vitro assembled chromatin.", "doi": "10.1016/j.dib.2016.05.057", "pmid": "27331114", "authors": ["Moritz Carl Völker-Albert", "Miriam Caroline Pusch", "Andreas Schmidt", "Axel Imhof"], "journal": "Data in brief", "year": 2016, "abstract": "Here, we use LC-MS/MS and SWATH-MS to describe the kinetics of in vitro assembled chromatin supported by an embryo extract prepared from preblastoderm Drosophila melanogaster embryos (DREX). This system allows easy manipulation of distinct aspects of chromatin assembly such as post-translational histone modifications, the levels of histone chaperones and the concentration of distinct DNA binding factors. In total, 480 proteins have been quantified as chromatin enriched factors and their binding kinetics have been monitored in the time course of 15 min, 1 h and 4 h of chromatin assembly. The data accompanying the manuscript on this approach, Völker-Albert et al., 2016 \"A quantitative proteomic analysis of in vitro assembled chromatin\" [1], has been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository with the dataset identifier submission number PRIDE: PXD002537 and PRIDE: PXD003445.", "claims": [{"id": "claim-method", "statement": "Data were searched against a combined forward/reversed database (special amino acids: KR) including common contaminants for false-discovery rate filtering of peptide and protein identifications (Dmel_all translation r5.57, 30305 entries).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27331114", "locator": "sections[12] \"Data analysis of data-dependent LC–MS experiments\" paragraph 2", "quote": "Data were searched against a combined forward/reversed database (special amino acids: KR) including common contaminants for false-discovery rate filtering of peptide and protein identifications (Dmel_all translation r5.57, 30305 entries)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data is within this article and uploaded to the ProteomeXchange Consortium webpage. Dataset identifier: PRIDE: PXD002537 and PRIDE: PXD003445.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27331114", "locator": "sections[2] \"table-wrap\" paragraph 1", "quote": "Data is within this article and uploaded to the ProteomeXchange Consortium webpage. Dataset identifier: PRIDE: PXD002537 and PRIDE: PXD003445."}], "state": "complete"}, {"id": "claim-target-result", "statement": "By means of DIA-MS in combination with a conservative statistical analysis, we were able to quantify 480 chromatin-enriched proteins compared to the negative control [1] (Fig. 1 D).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27331114", "locator": "sections[4] \"Data\" paragraph 5", "quote": "By means of DIA-MS in combination with a conservative statistical analysis, we were able to quantify 480 chromatin-enriched proteins compared to the negative control [1] (Fig. 1 D)."}, {"asset": "source:pmid:27331114", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The data accompanying the manuscript on this approach, Völker-Albert et al., 2016 “A quantitative proteomic analysis of in vitro assembled chromatin” [1], has been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository with the dataset identifier submission number PRIDE: PXD002537 and PRIDE: PXD003445."}, {"asset": "source:pmid:27331114", "locator": "sections[14] \"Statistical methods\" paragraph 2", "quote": "Data were handled with Perseus software."}, {"asset": "source:pmid:27331114", "locator": "sections[14] \"Statistical methods\" paragraph 3", "quote": "DIA-MS SWATH intensities were normalized to the total area sum within the MarkerView software (version 1.2.1.1). In order to compare different assembly times, the median of three biological replicates was calculated for each protein and each time point."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "By means of DIA-MS in combination with a conservative statistical analysis, we were able to quantify 480 chromatin-enriched proteins compared to the negative control [1] (Fig. 1 D).", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:27331114"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:27331114", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2016.05.057", "sha256": "sha256:20ad777e708622349035c4f844441af1338cc2622e1fd85908fe2cf0eb7f955c", "bytes": 19967, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2016.05.057", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4908269", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "False discovery rate (FDR) filtering", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Data were searched against a combined forward/reversed database (special amino acids: KR) including common contaminants for false-discovery rate filtering of peptide and protein identifications (Dmel_all translation r5.57, 30305 entries)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (False discovery rate (FDR) filtering), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": ["PRIDE: PXD002537 and PRIDE: PXD003445"], "resolved_accessions": [], "statements": ["Data is within this article and uploaded to the ProteomeXchange Consortium webpage. Dataset identifier: PRIDE: PXD002537 and PRIDE: PXD003445."], "basis": "The paper names PRIDE: PXD002537 and PRIDE: PXD003445, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:27331114"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:28:43Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 45718, "completion_tokens": 5089, "cached_tokens": 1816}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:27331114", "type": "paper", "label": "pmid:27331114"}, {"id": "source:pmid:27331114", "type": "manuscript", "label": "PMID 27331114 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:27331114", "type": "paper", "label": "pmid:27331114"}, {"id": "source:pmid:27331114", "type": "manuscript", "label": "PMID 27331114 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-27331114", "type": "extraction", "used": ["source:pmid:27331114"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:27331114", "parent_hash": "sha256:05d77dcab3523567eed67dcd5e467660b5d6742ed96e4307edd36e7987792c83", "fork_of": null, "generation": 5}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Here, we use LC-MS/MS and SWATH-MS to describe the kinetics of in", "nalysis Assembled chromatin was subjected to mass spectrometry analysis. 90% of the chromatin bound protein", ") and desalted using C18 stage tips prior to mass spectrometry analyses and redissolved in 0.2% TFA [2]. Th", ", Völker-Albert et al., 2016 \"A quantitative proteomic analysis of in vitro assembled chromatin\" [1"], "order_basis": "paper_text_order:54", "id": "assay:1"}]}