← All .science files
pmid:26697372
Expression profiling of human melanocytes in response to UV-B irradiation.
Saioa López · Isabel Smith-Zubiaga · Santos Alonso
Genomics data · 2015 doi:10.1016/j.gdata.2015.09.013
Paper
complete
Experiment
complete
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 · 3 items
claims array · 3 items
[0] object · 6 fields
[1] object · 6 fields
[2] object · 6 fields
evidence array · 3 items
[0] object · 3 fields
[1] 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 · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
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 · 0 items
data object · 3 fields
assets array · 3 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 82 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 9 items
[0] array · 2 items
[1] array · 2 items
[2] array · 2 items
[3] array · 2 items
[4] array · 2 items
[5] array · 2 items
[6] array · 2 items
[7] array · 2 items
[8] array · 2 items
gaps array · 2 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 · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 3 items
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 · 7 items
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26697372", "kind": "science-record", "revision": 4, "content_hash": "sha256:15faad670152946df5e04d5c788a9d4383b58ffeaa27e7a01811d47bd7e9c434", "created_at": "2026-11-01T15:40:15Z", "updated_at": "2026-11-01T21:20:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Expression profiling of human melanocytes in response to UV-B irradiation.", "doi": "10.1016/j.gdata.2015.09.013", "pmid": "26697372", "authors": ["Saioa López", "Isabel Smith-Zubiaga", "Santos Alonso"], "journal": "Genomics data", "year": 2015, "abstract": "A comprehensive gene expression analysis of human melanocytes was performed assessing the transcriptional profile of dark melanocytes (DM) and light melanocytes (LM) at basal conditions and after UV-B irradiation at different time points (6, 12 and 24 h), and in culture with different keratinocyte-conditioned media (KCM + and KCM -). The data, previously published in [1], have been deposited in NCBI's Gene Expression Omnibus (GEO accession number: GSE70280).", "claims": [{"id": "claim-method", "statement": "The expression profiles of melanocytes were compared with SAM (Significance Analysis of Microarrays) [3] using two class non-pairwise comparisons and 500 permutations in each test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697372", "locator": "sections[7] \"Statistical analyses\" paragraph 2", "quote": "The expression profiles of melanocytes were compared with SAM (Significance Analysis of Microarrays) [3] using two class non-pairwise comparisons and 500 permutations in each test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data, previously published in [1], have been deposited in NCBI's Gene Expression Omnibus (GEO accession number: GSE70280).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697372", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data, previously published in [1], have been deposited in NCBI's Gene Expression Omnibus (GEO accession number: GSE70280)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A comprehensive gene expression analysis was performed across dark and light melanocytes at basal conditions and after UV-B irradiation at 6, 12, and 24 h, with KCM+ and KCM− conditions; the source data were deposited in NCBI Gene Expression Omnibus under accession GSE70280, with direct access via the GEO accession URL.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26697372", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A comprehensive gene expression analysis of human melanocytes was performed assessing the transcriptional profile of dark melanocytes (DM) and light melanocytes (LM) at basal conditions and after UV-B irradiation at different time points (6, 12 and 24 h), and in culture with different keratinocyte-conditioned media (KCM + and KCM −)."}, {"asset": "source:pmid:26697372", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data, previously published in [1], have been deposited in NCBI's Gene Expression Omnibus (GEO accession number: GSE70280)."}, {"asset": "source:pmid:26697372", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70280."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A comprehensive gene expression analysis was performed across dark and light melanocytes at basal conditions and after UV-B irradiation at 6, 12, and 24 h, with KCM+ and KCM− conditions; the source data were deposited in NCBI Gene Expression Omnibus under accession GSE70280, with direct access via the GEO accession URL.", "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:26697372"], "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": "complete", "blocked_on": null, "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": ["data:geo:GSE70280"], "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": ["data:geo:GSE70280"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26697372", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.09.013", "sha256": "sha256:73650f98661449043676a0707353bc5415e7db73a6e278d5b9973dc053a40465", "bytes": 7336, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.09.013", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4664746", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE70280", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70280", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE70280", "version": null, "note": "The data, previously published in [1], have been deposited in NCBI's Gene Expression Omnibus (GEO accession number: GSE70280).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data, previously published in [1], have been deposited in NCBI's Gene Expression Omnibus (GEO accession number: GSE70280).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1722804", "GSM1722805", "GSM1722806", "GSM1722807", "GSM1722808", "GSM1722809", "GSM1722810", "GSM1722811", "GSM1722812", "GSM1722813", "GSM1722814", "GSM1722815", "GSM1722816", "GSM1722817", "GSM1722818", "GSM1722819", "GSM1722820", "GSM1722821", "GSM1722822", "GSM1722823", "GSM1722824", "GSM1722825", "GSM1722826", "GSM1722827", "GSM1722828", "GSM1722829", "GSM1722830", "GSM1722831", "GSM1722832", "GSM1722833", "GSM1722834", "GSM1722835", "GSM1722836", "GSM1722837", "GSM1722838", "GSM1722839", "GSM1722840", "GSM1722841", "GSM1722842", "GSM1722843", "GSM1722844", "GSM1722845", "GSM1722846", "GSM1722847", "GSM1722848", "GSM1722849", "GSM1722850", "GSM1722851", "GSM1722852", "GSM1722853", "GSM1722854", "GSM1722855", "GSM1722856", "GSM1722857", "GSM1722858", "GSM1722859", "GSM1722860", "GSM1722861", "GSM1722862", "GSM1722863", "GSM1722864", "GSM1722865", "GSM1722866", "GSM1722867", "GSM1722868", "GSM1722869", "GSM1722870", "GSM1722871", "GSM1722872", "GSM1722873", "GSM1722874", "GSM1722875", "GSM1722876", "GSM1722877", "GSM1722878", "GSM1722879", "GSM1722880", "GSM1722881", "GSM1722882", "GSM1722883", "GSM1722884", "GSM1722885"], "sample_count": 82, "group_sizes": null, "group_sizes_basis": null, "platform": "14550", "taxon": "Homo sapiens", "title": "Comparison of the Transcriptional Profiles of Melanocytes from Dark and Light Skinned Individuals under Basal Conditions and Following Ultraviolet-B Irradiation", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26697372:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cf2b4746d9834032149ecc21d534c1486c5b642fb73b3924f4b0b71c80e2eb5f", "bytes": 1060, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0010", "version": null, "note": null, "structure": {"pmcid": "PMC4664746", "section_index": 1, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Specifications", ""], ["Organism/cell line/tissue", "Homo sapiens/epidermal melanocytes/skin"], ["Sex", "Male"], ["Sequencer or array type", "Agilent-028004 SurePrint G3 Human GE 8 × 60K Microarrays"], ["Data format", "Raw data: TXT; normalized data: SOFT, MINiML and TXT"], ["Experimental factors", "Skin pigmentation (light vs dark pigmented), time after UV-B irradiation (0, 6, 12 and 24 h) and keratinocyte-conditioned media (KCM + vs KCM −)"], ["Experimental features", "Gene expression analysis of dark melanocytes (DM) and light melanocytes (LM) at basal conditions and after UV-B at different time points (6, 12 and 24 h), and in culture with different keratinocyte-conditioned media (KCM + and KCM −)"], ["Consent", "Data is publicly available and open for re-use given appropriate citation"], ["Sample source location", "Cells were purchased from Cascade Biologics (Life Technologies) and Innoprot (see Table 1)"]], "row_count": 9, "column_count": 2, "numeric_cells": 4, "header_rows": 1, "locator": "section[1]/table-wrap[1]#t0010"}}], "gaps": ["asset:data:geo:GSE70280 not downloaded", "asset:data:geo:GSE70280 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Significance Analysis of Microarrays (SAM)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The expression profiles of melanocytes were compared with SAM (Significance Analysis of Microarrays) [3] using two class non-pairwise comparisons and 500 permutations in each test."}}], "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": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Significance Analysis of Microarrays (SAM)), 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": "R1", "reachable": true, "accessions": ["GSE70280"], "resolved_accessions": ["GSE70280"], "statements": ["The data, previously published in [1], have been deposited in NCBI's Gene Expression Omnibus (GEO accession number: GSE70280)."], "basis": "The paper names GSE70280 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26697372", "data:geo:GSE70280", "asset:table:pmid:26697372:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE70280"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:52Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 19422, "completion_tokens": 2235, "cached_tokens": 1832}}, "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:26697372", "type": "paper", "label": "pmid:26697372"}, {"id": "source:pmid:26697372", "type": "manuscript", "label": "PMID 26697372 full text"}, {"id": "data:geo:GSE70280", "type": "dataset", "label": "GEO GSE70280"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26697372", "type": "paper", "label": "pmid:26697372"}, {"id": "source:pmid:26697372", "type": "manuscript", "label": "PMID 26697372 full text"}, {"id": "data:geo:GSE70280", "type": "dataset", "label": "GEO GSE70280"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26697372", "type": "extraction", "used": ["source:pmid:26697372"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE70280", "type": "accession_resolution", "used": ["data:geo:GSE70280"], "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:26697372", "parent_hash": "sha256:503268a543099caa59ac944425b6c45c437d74943ed67de6f76d37db8e379842", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE70280 licence not read", "asset:data:geo:GSE70280 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}