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Altered neutrophil and granulopoiesis biology underlie a poor outcome sepsis endotype

Type: Transcriptome Analysis
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 4 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001010927	This dataset contains raw sequencing files associated with the paper "Neutrophils and emergency granulopoiesis drive immune suppression and an extreme response endotype during sepsis" (https://doi.org/10.1038/s41590-023-01490-5). It is composed of two experiments, which are as follows: 1. Single-cell profiling of whole blood leukocytes: This experiment comprises sequencing files generated using the BD Rhapsody single-cell multi-omics profiling (RNA + protein) platform. This platform was used to profile the whole blood leukocyte population in a cohort of sepsis patients, cardiac surgery controls and healthy controls. There are 48 samples and four files per sample: two paired-end FASTQ files (R1 and R2) corresponding to the RNA-seq library, and two paired-end FASTQ files (R1 and R2) corresponding to the protein profiling (ADT-based AbSeq) library. 2. Single-cell profiling of circulating HSPCs: This experiment comprises sequencing files generated using the 10X single-cell multi-omics (RNA-seq + ATAC-seq) profiling platform. This platform was used to profile circulating HSPCs in a cohort of sepsis patients and healthy controls. There are 5 samples (or plexes), each of which consists of a pool of individuals for whom cells were multiplexed and sequenced as a single sample. There are four files per sample: two paired-end FASTQ files (R1 and R2) corresponding to the RNA-seq library, and two paired-end FASTQ files (R1 and R2) corresponding to the ATAC-seq library. Because these samples consists of multiplexed pools, index files are also provided. These can be used for sample deconvolution using the Cell Ranger pipeline. NOTE: Due to EGA's constrains in the number of files permitted per sample, index files (I1 and I2) for the HSPC data set are provided as a separate experiment named "FASTQ index files (I1 and I2) for deconvolution of 10X single-cell multiomics libraries".	Illumina NovaSeq 6000	106

Publications	Citations
Demultiplexing of single-cell RNA-sequencing data using interindividual variation in gene expression. Nassiri I, Kwok AJ, Bhandari A, Bull KR, Garner LC, Klenerman P, Webber C, Parkkinen L, Lee AW, Wu Y, Fairfax B, Knight JC, Buck D, Piazza P. Bioinform Adv 4: 2024 vbae085	5
A transcriptome-based risk model in sepsis enables prognostic prediction and drug repositioning. Long Q, Ye H, Song S, Li J, Wu J, Mao J, Li R, Ke Li, Gao Z, Zheng Y. iScience 27: 2024 111277	1
Sphingolipid metabolism-related genes as diagnostic markers in pneumonia-induced sepsis: the AUG model. Wu J, Li X, Chen Z, Lin Y, Long Q, Jiang M, Hu X, Song S, Ye H, Li J, Wu F, Zheng J, Wang M, Gao Z, Ning P, Zheng Y. Sci Rep 15: 2025 17552	1
Identifying propionate metabolism-related genes as biomarkers of sepsis development and therapeutic targets. Yang L, Shang W, Chen D, Qian H, Zhang S, Pan X, Huang S, Liu J, Chen D. Sci Rep 15: 2025 24531	2