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Neutrophils and emergency granulopoiesis drive immune suppression and an extreme response endotype during sepsis

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".

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Data access policy associated with the publication "Neutrophils and emergency granulopoiesis drive immune suppression and an extreme response endotype during sepsis" (https://doi.org/10.1038/s41590-023-01490-5).

Same as for https://ega-archive.org/dacs/EGAC01000000009

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001006283 Transcriptome Analysis

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00008090673 fastq.gz 26.1 GB
EGAF00008090674 fastq.gz 27.6 GB
EGAF00008090675 fastq.gz 21.4 GB
EGAF00008090676 fastq.gz 22.5 GB
EGAF00008090677 fastq.gz 24.2 GB
EGAF00008090678 fastq.gz 25.5 GB
EGAF00008090679 fastq.gz 25.4 GB
EGAF00008090680 fastq.gz 26.3 GB
EGAF00008090681 fastq.gz 23.4 GB
EGAF00008090682 fastq.gz 24.2 GB
EGAF00008090683 fastq.gz 25.2 GB
EGAF00008090684 fastq.gz 26.1 GB
EGAF00008090685 fastq.gz 25.7 GB
EGAF00008090686 fastq.gz 27.0 GB
EGAF00008090687 fastq.gz 21.1 GB
EGAF00008090688 fastq.gz 22.0 GB
EGAF00008090689 fastq.gz 2.6 GB
EGAF00008090690 fastq.gz 2.6 GB
EGAF00008090691 fastq.gz 2.7 GB
EGAF00008090692 fastq.gz 2.8 GB
EGAF00008090693 fastq.gz 2.8 GB
EGAF00008090694 fastq.gz 2.8 GB
EGAF00008090695 fastq.gz 2.3 GB
EGAF00008090696 fastq.gz 2.3 GB
EGAF00008090697 fastq.gz 2.5 GB
EGAF00008090698 fastq.gz 2.5 GB
EGAF00008090699 fastq.gz 2.6 GB
EGAF00008090700 fastq.gz 2.7 GB
EGAF00008090701 fastq.gz 2.5 GB
EGAF00008090702 fastq.gz 2.5 GB
EGAF00008090703 fastq.gz 2.8 GB
EGAF00008090704 fastq.gz 2.8 GB
EGAF00008090705 fastq.gz 25.5 GB
EGAF00008090706 fastq.gz 27.0 GB
EGAF00008090707 fastq.gz 21.2 GB
EGAF00008090708 fastq.gz 22.3 GB
EGAF00008090709 fastq.gz 21.9 GB
EGAF00008090710 fastq.gz 22.6 GB
EGAF00008090711 fastq.gz 22.4 GB
EGAF00008090712 fastq.gz 23.5 GB
EGAF00008090713 fastq.gz 19.0 GB
EGAF00008090714 fastq.gz 20.3 GB
EGAF00008090715 fastq.gz 22.3 GB
EGAF00008090716 fastq.gz 23.6 GB
EGAF00008090717 fastq.gz 25.3 GB
EGAF00008090718 fastq.gz 26.5 GB
EGAF00008090719 fastq.gz 20.7 GB
EGAF00008090720 fastq.gz 21.5 GB
EGAF00008090721 fastq.gz 2.3 GB
EGAF00008090722 fastq.gz 2.3 GB
EGAF00008090723 fastq.gz 2.2 GB
EGAF00008090724 fastq.gz 2.2 GB
EGAF00008090725 fastq.gz 2.4 GB
EGAF00008090726 fastq.gz 2.4 GB
EGAF00008090727 fastq.gz 1.9 GB
EGAF00008090728 fastq.gz 1.9 GB
EGAF00008090729 fastq.gz 1.8 GB
EGAF00008090730 fastq.gz 1.8 GB
EGAF00008090731 fastq.gz 2.3 GB
EGAF00008090732 fastq.gz 2.3 GB
EGAF00008090733 fastq.gz 2.2 GB
EGAF00008090734 fastq.gz 2.2 GB
EGAF00008090735 fastq.gz 2.5 GB
EGAF00008090736 fastq.gz 2.5 GB
EGAF00008090737 fastq.gz 22.9 GB
EGAF00008090738 fastq.gz 24.2 GB
EGAF00008090739 fastq.gz 22.3 GB
EGAF00008090740 fastq.gz 23.6 GB
EGAF00008090741 fastq.gz 20.4 GB
EGAF00008090742 fastq.gz 21.7 GB
EGAF00008090743 fastq.gz 28.4 GB
EGAF00008090744 fastq.gz 29.5 GB
EGAF00008090745 fastq.gz 17.2 GB
EGAF00008090746 fastq.gz 18.4 GB
EGAF00008090747 fastq.gz 22.4 GB
EGAF00008090748 fastq.gz 23.8 GB
EGAF00008090749 fastq.gz 19.1 GB
EGAF00008090750 fastq.gz 20.6 GB
EGAF00008090751 fastq.gz 17.5 GB
EGAF00008090752 fastq.gz 18.6 GB
EGAF00008090753 fastq.gz 1.9 GB
EGAF00008090754 fastq.gz 1.9 GB
EGAF00008090755 fastq.gz 2.1 GB
EGAF00008090756 fastq.gz 2.2 GB
EGAF00008090757 fastq.gz 2.3 GB
EGAF00008090758 fastq.gz 2.3 GB
EGAF00008090759 fastq.gz 2.0 GB
EGAF00008090760 fastq.gz 2.0 GB
EGAF00008090761 fastq.gz 2.0 GB
EGAF00008090762 fastq.gz 2.1 GB
EGAF00008090763 fastq.gz 2.1 GB
EGAF00008090764 fastq.gz 2.1 GB
EGAF00008090765 fastq.gz 2.2 GB
EGAF00008090766 fastq.gz 2.2 GB
EGAF00008090767 fastq.gz 1.9 GB
EGAF00008090768 fastq.gz 1.9 GB
EGAF00008090769 fastq.gz 22.4 GB
EGAF00008090770 fastq.gz 23.6 GB
EGAF00008090771 fastq.gz 18.8 GB
EGAF00008090772 fastq.gz 19.9 GB
EGAF00008090773 fastq.gz 20.0 GB
EGAF00008090774 fastq.gz 21.1 GB
EGAF00008090775 fastq.gz 20.7 GB
EGAF00008090776 fastq.gz 21.8 GB
EGAF00008090777 fastq.gz 16.1 GB
EGAF00008090778 fastq.gz 17.5 GB
EGAF00008090779 fastq.gz 22.3 GB
EGAF00008090780 fastq.gz 23.9 GB
EGAF00008090781 fastq.gz 23.6 GB
EGAF00008090782 fastq.gz 24.8 GB
EGAF00008090783 fastq.gz 22.5 GB
EGAF00008090784 fastq.gz 23.2 GB
EGAF00008090785 fastq.gz 2.6 GB
EGAF00008090786 fastq.gz 2.7 GB
EGAF00008090787 fastq.gz 2.5 GB
EGAF00008090788 fastq.gz 2.5 GB
EGAF00008090789 fastq.gz 2.4 GB
EGAF00008090790 fastq.gz 2.4 GB
EGAF00008090791 fastq.gz 2.1 GB
EGAF00008090792 fastq.gz 2.1 GB
EGAF00008090793 fastq.gz 1.9 GB
EGAF00008090794 fastq.gz 1.9 GB
EGAF00008090795 fastq.gz 2.5 GB
EGAF00008090796 fastq.gz 2.5 GB
EGAF00008090797 fastq.gz 2.4 GB
EGAF00008090798 fastq.gz 2.4 GB
EGAF00008090799 fastq.gz 2.6 GB
EGAF00008090800 fastq.gz 2.6 GB
EGAF00008090801 fastq.gz 20.5 GB
EGAF00008090802 fastq.gz 21.7 GB
EGAF00008090803 fastq.gz 18.4 GB
EGAF00008090804 fastq.gz 19.9 GB
EGAF00008090805 fastq.gz 18.6 GB
EGAF00008090806 fastq.gz 19.8 GB
EGAF00008090807 fastq.gz 19.5 GB
EGAF00008090808 fastq.gz 20.5 GB
EGAF00008090809 fastq.gz 19.2 GB
EGAF00008090810 fastq.gz 20.6 GB
EGAF00008090811 fastq.gz 18.4 GB
EGAF00008090812 fastq.gz 19.8 GB
EGAF00008090813 fastq.gz 20.9 GB
EGAF00008090814 fastq.gz 22.6 GB
EGAF00008090815 fastq.gz 19.3 GB
EGAF00008090816 fastq.gz 20.4 GB
EGAF00008090817 fastq.gz 2.2 GB
EGAF00008090818 fastq.gz 2.2 GB
EGAF00008090819 fastq.gz 2.1 GB
EGAF00008090820 fastq.gz 2.1 GB
EGAF00008090821 fastq.gz 2.1 GB
EGAF00008090822 fastq.gz 2.1 GB
EGAF00008090823 fastq.gz 1.7 GB
EGAF00008090824 fastq.gz 1.7 GB
EGAF00008090825 fastq.gz 1.7 GB
EGAF00008090826 fastq.gz 1.7 GB
EGAF00008090827 fastq.gz 1.9 GB
EGAF00008090828 fastq.gz 1.9 GB
EGAF00008090829 fastq.gz 1.7 GB
EGAF00008090830 fastq.gz 1.7 GB
EGAF00008090831 fastq.gz 2.0 GB
EGAF00008090832 fastq.gz 2.0 GB
EGAF00008090833 fastq.gz 22.4 GB
EGAF00008090834 fastq.gz 24.0 GB
EGAF00008090835 fastq.gz 17.9 GB
EGAF00008090836 fastq.gz 19.4 GB
EGAF00008090837 fastq.gz 19.3 GB
EGAF00008090838 fastq.gz 20.7 GB
EGAF00008090839 fastq.gz 21.8 GB
EGAF00008090840 fastq.gz 23.4 GB
EGAF00008090841 fastq.gz 19.4 GB
EGAF00008090842 fastq.gz 20.9 GB
EGAF00008090843 fastq.gz 21.2 GB
EGAF00008090844 fastq.gz 22.9 GB
EGAF00008090845 fastq.gz 21.8 GB
EGAF00008090846 fastq.gz 23.5 GB
EGAF00008090847 fastq.gz 21.4 GB
EGAF00008090848 fastq.gz 22.5 GB
EGAF00008090849 fastq.gz 2.1 GB
EGAF00008090850 fastq.gz 2.1 GB
EGAF00008090851 fastq.gz 2.1 GB
EGAF00008090852 fastq.gz 2.1 GB
EGAF00008090853 fastq.gz 2.1 GB
EGAF00008090854 fastq.gz 2.1 GB
EGAF00008090855 fastq.gz 1.8 GB
EGAF00008090856 fastq.gz 1.8 GB
EGAF00008090857 fastq.gz 1.9 GB
EGAF00008090858 fastq.gz 1.9 GB
EGAF00008090859 fastq.gz 2.1 GB
EGAF00008090860 fastq.gz 2.1 GB
EGAF00008090861 fastq.gz 2.0 GB
EGAF00008090862 fastq.gz 2.1 GB
EGAF00008090863 fastq.gz 2.1 GB
EGAF00008090864 fastq.gz 2.1 GB
EGAF00008090865 fastq.gz 1.6 GB
EGAF00008090866 fastq.gz 3.6 GB
EGAF00008090867 fastq.gz 7.3 GB
EGAF00008090868 fastq.gz 7.3 GB
EGAF00008090869 fastq.gz 3.1 GB
EGAF00008090870 fastq.gz 3.3 GB
EGAF00008090871 fastq.gz 54.4 GB
EGAF00008090872 fastq.gz 45.1 GB
EGAF00008090873 fastq.gz 1.7 GB
EGAF00008090874 fastq.gz 4.0 GB
EGAF00008090875 fastq.gz 8.0 GB
EGAF00008090876 fastq.gz 8.2 GB
EGAF00008090877 fastq.gz 3.4 GB
EGAF00008090878 fastq.gz 3.6 GB
EGAF00008090879 fastq.gz 62.0 GB
EGAF00008090880 fastq.gz 49.6 GB
EGAF00008090881 fastq.gz 1.8 GB
EGAF00008090882 fastq.gz 4.1 GB
EGAF00008090883 fastq.gz 8.2 GB
EGAF00008090884 fastq.gz 8.3 GB
EGAF00008090885 fastq.gz 3.6 GB
EGAF00008090886 fastq.gz 3.7 GB
EGAF00008090887 fastq.gz 64.7 GB
EGAF00008090888 fastq.gz 52.4 GB
EGAF00008090889 fastq.gz 1.9 GB
EGAF00008090890 fastq.gz 4.4 GB
EGAF00008090891 fastq.gz 8.7 GB
EGAF00008090892 fastq.gz 8.7 GB
EGAF00008090893 fastq.gz 3.5 GB
EGAF00008090894 fastq.gz 3.7 GB
EGAF00008090895 fastq.gz 60.5 GB
EGAF00008090896 fastq.gz 49.3 GB
EGAF00008090897 fastq.gz 1.6 GB
EGAF00008090898 fastq.gz 3.7 GB
EGAF00008090899 fastq.gz 7.5 GB
EGAF00008090900 fastq.gz 7.6 GB
EGAF00008090901 fastq.gz 3.5 GB
EGAF00008090902 fastq.gz 3.4 GB
EGAF00008090903 fastq.gz 57.5 GB
EGAF00008090904 fastq.gz 46.8 GB
232 Files (3.0 TB)