Data Card: Septic Shock Early Therapy Response Whole-Blood RNA-seq Dataset (GSE110487)

Summary

Expression + sample metadata + feature metadata for GSE110487, a whole-blood RNA-seq study of septic shock patients profiled for transcriptomic differences between early responders and non-responders to supportive hemodynamic therapy, assessed by SOFA score improvement within the first 48 hours of ICU admission.

Source accession

Accession	N (samples)	N (patients)	Platform	Retrieval source
GSE110487	62	31 (17 responders, 14 non-responders)	Illumina Genome Analyzer IIx (GPL10999, 6 samples) + Illumina HiSeq 2500 (GPL16791, 56 samples)	NCBI GEO

Each patient contributed 2 samples: T1 (within 16 hours of ICU admission) and T2 (within 48 hours). This SuperSeries splits its 62 samples across two sequencing platforms — both were combined to build sample metadata, since NCBI's RNA-seq reprocessing counts file pools both platforms into one matrix.

Files

• sample_metadata.parquet — one row per sample: sample_id, patient_id, response_to_treatment (logical; TRUE = Responder), timepoint (T1/T2)
• feature_metadata.parquet — one row per gene (GeneID, NCBI Entrez Gene ID): NCBI's GRCh38.p13 gene annotation file (Human.GRCh38.p13.annot.tsv.gz), matched to the same reprocessing build as the expression data
• expression.parquet — single file, long format: GeneID, sample_id, value

Sample metadata field notes

• response_to_treatment is a per-patient classification (Responder vs. Not Responder, defined by SOFA score improvement within 48 hours), constant across a patient's T1/T2 samples — unlike some other datasets in this collection, this label does not vary by timepoint.
• timepoint is T1 (within 16h of ICU admission) or T2 (within 48h). 28 T1 samples, 34 T2 samples — not perfectly balanced, worth noting if used in a paired analysis.
• All 31 patients have exactly 2 samples (one T1, one T2); no missing timepoints.
• No age or sex data available in the accession's sample-level metadata.

Expression value processing

Raw, un-normalized gene-level counts, from NCBI's own RNA-seq reprocessing pipeline (GRCh38.p13 realignment). No filtering or normalization has been applied.

Provenance / reproducibility

See pull_gse110487.R.