{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Carlos Ortiz-Ramirez"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15719"],"description":["This work reports on a new methodology that allows processing immune cells (PBMCs) from blood in challenging settings (clinical or remote rural areas) for downstream single cell sequencing. Thus, allowing the inclusion of underserved communities in population-level immune profiling projects and comprehensive cellular atlases.   Current methodologies for PBMCs isolation and cryopreservation cannot be deployed in remote areas with limited infrastructure, leaving many populations from the global south absent from those initiatives. The methodology reported in this manuscript, which we call SiteCELL, circumvents those limitations and can be implemented with minimal equipment and without electricity."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Sequencing was done using the Illumina Novaseq X plus platform. In brief, libraries were normalized and pooled in the appropriate molarity to be loaded on a flow cell together with buffers and reagents provided in NovaSeq X sequencing kit. Sequencing was pair-end 150bp. The PhinX spike-in control was added at concentration ranging from 1% to 5% depending on the library. Sequenced data was demultiplexed based on 10X genomics index sequences before proceeding to QC analyses.","Library Construction - Library preparation followed the standard 10x Genomics protocol, including fragmentation, end repair, A-tailing, adaptor ligation, and PCR amplification. Quality control of the libraries was performed using Qubit® Fluorometry for quantification and Agilent 2100 Bioanalyzer or TapeStation 4150 capillary electrophoresis for size distribution analysis.","Nucleic Acid Extraction - For single cell RNA sequencing, cells from different participants were pooled together based on equal cell ratios. To maximize genetic diversity and minimize processing costs, four individuals were selected for each multiplexed library construction. Cryovials from the selected individuals were thawed, and cells were washed before a viability assessment was performed using a microscope-based cell count. The Chromium Single Cell 3’ Library & Gel Bead Kit (10x Genomics) was used to generate single cell libraries. Each participant contributed approximately 5,000 cells per multiplex, targeting a recovery of around 20,000 cells per well on the 10x Genomics Chip M. After generating gel bead-in-emulsion (GEM) droplets, the reverse transcription and cDNA amplification was performed within the droplets, incorporating unique molecular identifiers (UMIs) and cell barcodes.","Sample Collection - Two types of biological samples were collected from each participant: (1) a blood sample, at least one 6 ml blood sample was drawn using a lavender-top Vacutainer tube containing EDTA; (2) a saliva sample collected using Oracollect®•DNA OCR-100 swab (DNA Genotek), designed for non-invasive collection of high-quality DNA from oral cells. The swab and blood tube were both labeled with the participant's identification number."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw scRNA-seq reads were processed using Cell Ranger (v8.3.0, 10x Genomics) with default parameters against the GRCh38-2024-A human reference genome (Ensembl), resulting in the generation of gene-by-cell expression matrices. Mapping quality was assessed through standard Cell Ranger summary metrics, including the fraction of reads confidently mapped to the transcriptome, sequencing saturation, mean reads per cell, and mean genes detected per cell. BAM files were generated for each multiplexed pool for subsequent demultiplexing and downstream analyses."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Carlos Ortiz-Ramirez"],"additional_accession":[]},"is_claimable":false,"name":"SiteCELL enables on-site PBMCs purification and cryopreservation for immune single cell profiling of diverse ancestries","description":"This work reports on a new methodology that allows processing immune cells (PBMCs) from blood in challenging settings (clinical or remote rural areas) for downstream single cell sequencing. Thus, allowing the inclusion of underserved communities in population-level immune profiling projects and comprehensive cellular atlases.   Current methodologies for PBMCs isolation and cryopreservation cannot be deployed in remote areas with limited infrastructure, leaving many populations from the global south absent from those initiatives. The methodology reported in this manuscript, which we call SiteCELL, circumvents those limitations and can be implemented with minimal equipment and without electricity.","dates":{"release":"2026-04-02T00:00:00Z","modification":"2026-04-02T01:05:01.7Z","creation":"2025-10-15T09:38:09.923Z"},"accession":"E-MTAB-15719","cross_references":{"ENA":["ERP182203"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}