Transcriptomic dataset from peripheral white blood cells of beef heifers at weaning.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36969977", "kind": "science-record", "revision": 4, "content_hash": "sha256:0ea80e66d207b7528676f3ced85f08e000147f7fbec76a262aa54029be0ccb2b", "created_at": "2026-11-01T19:01:37Z", "updated_at": "2026-11-01T22:51:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptomic dataset from peripheral white blood cells of beef heifers at weaning.", "doi": "10.1016/j.dib.2023.109046", "pmid": "36969977", "authors": ["Priyanka Banerjee", "Wellison J S Diniz", "Soren P Rodning", "Paul W Dyce"], "journal": "Data in brief", "year": 2023, "abstract": "Reproductive failure of replacement breeding animals is one of the leading causes of loss to the beef production industry. The losses are further increased due to the inability to diagnose the reproductive potential of the beef heifer prior to the breeding season until the pregnancy outcome. To overcome this problem, a system to discriminate beef heifers with varying reproductive potential as early and accurately as possible is demanded. The omics technologies, such as transcriptomics, could predict the future reproductive potential of beef heifers. Therefore, this manuscript provides the gene expression profile dataset using RNA-Seq identified from peripheral white blood cells (PWBC) of beef heifers at weaning. To accomplish this, the blood samples were collected at the time of weaning, processed to extract the PWBC pellet and stored at - 80 °C until further processing. After the breeding protocol (artificial insemination (AI) followed by natural bull service) and pregnancy diagnosis, the heifers that were pregnant to AI (n = 8) or remained open (n = 7) were utilized for this study. Total RNA was extracted from PWBC collected at the time of weaning from these samples and subjected to sequencing using the Illumina Nova-Seq platform. High-quality sequencing data was analyzed using a bioinformatic workflow based on FastQC and MultiQC for quality control, STAR for read alignment, and DESeq2 for differential expression analysis. Genes were considered significantly differentially expressed after adjustment with Bonferroni correction (padj ≤ 0.05) and absolute (log2 fold change) ≥ 0.5. Raw and processed RNA-Seq data were deposited and made publicly available on the gene expression omnibus database (GEO; GSE221903). To our knowledge, this is the first dataset investigating the change in the gene expression level as early as weaning to predict the future reproductive outcome in beef heifers. Interpretation of the main findings based on this data is reported in a research article titled \"mRNA Signatures in Peripheral White Blood Cells Predicts Reproductive Potential in Beef Heifers at Weaning\" [1].", "claims": [{"id": "claim-method", "statement": "The filtered raw gene counts were then subjected to differential expression analysis using DESeq2 v1.26.0 [7].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36969977", "locator": "sections[11] \"Data Analysis\" paragraph 2", "quote": "The filtered raw gene counts were then subjected to differential expression analysis using DESeq2 v1.26.0 [7]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Transcriptome profiling from peripheral white blood cells in fertile and subfertile beef heifers at weaning (Original data) (NCBI).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36969977", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "Transcriptome profiling from peripheral white blood cells in fertile and subfertile beef heifers at weaning (Original data) (NCBI)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:36969977"], "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:GSE221903"], "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:GSE221903"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36969977", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2023.109046", "sha256": "sha256:e1534fa592c3a85e8b4ed555d1f5e6e2eda795ea78518b02e037cefe862a3772", "bytes": 15194, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2023.109046", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10034631", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE221903", "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=GSE221903", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE221903", "version": null, "note": "Transcriptome profiling from peripheral white blood cells in fertile and subfertile beef heifers at weaning (Original data) (NCBI).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Transcriptome profiling from peripheral white blood cells in fertile and subfertile beef heifers at weaning (Original data) (NCBI).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM6909159", "GSM6909160", "GSM6909161", "GSM6909162", "GSM6909163", "GSM6909164", "GSM6909165", "GSM6909166", "GSM6909167", "GSM6909168", "GSM6909169", "GSM6909170", "GSM6909171", "GSM6909172", "GSM6909173"], "sample_count": 15, "group_sizes": null, "group_sizes_basis": null, "platform": "26012", "taxon": "Bos taurus", "title": "Transcriptome profiling from peripheral white blood cells in fertile and subfertile beef heifers at weaning", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE221903 not downloaded", "asset:data:geo:GSE221903 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "deseq2", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The filtered raw gene counts were then subjected to differential expression analysis using DESeq2 v1.26.0 [7]."}}], "targets": [], "gaps": []}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: deseq2."}, "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": ["GSE221903"], "resolved_accessions": ["GSE221903"], "statements": ["Transcriptome profiling from peripheral white blood cells in fertile and subfertile beef heifers at weaning (Original data) (NCBI)."], "basis": "The paper names GSE221903 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:36969977", "data:geo:GSE221903"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE221903"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:34:46Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 5401, "completion_tokens": 668, "cached_tokens": 0}}, "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:36969977", "type": "paper", "label": "pmid:36969977"}, {"id": "source:pmid:36969977", "type": "manuscript", "label": "PMID 36969977 full text"}, {"id": "data:geo:GSE221903", "type": "dataset", "label": "GEO GSE221903"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36969977", "type": "paper", "label": "pmid:36969977"}, {"id": "source:pmid:36969977", "type": "manuscript", "label": "PMID 36969977 full text"}, {"id": "data:geo:GSE221903", "type": "dataset", "label": "GEO GSE221903"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36969977", "type": "extraction", "used": ["source:pmid:36969977"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE221903", "type": "accession_resolution", "used": ["data:geo:GSE221903"], "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:36969977", "parent_hash": "sha256:7850594028b81d19f096121f82ce1f9303bb761f82a68510325064dcb61e4827", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE221903 licence not read", "asset:data:geo:GSE221903 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Transcriptomic dataset from peripheral white blood cells of", "is demanded. The omics technologies, such as transcriptomics, could predict the future reproductive poten", "es the gene expression profile dataset using RNA-Seq identified from peripheral white blood cells", "(log2 fold change) ≥ 0.5. Raw and processed RNA-Seq data were deposited and made publicly availa"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The filtered raw gene counts were then subjected to differential expression analysis using DESeq2 v1.26.0 [7]."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}