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Sample GSM6730093 Query DataSets for GSM6730093
Status Public on Sep 27, 2023
Title Child3_Day0
Sample type SRA
 
Source name blood
Organism Homo sapiens
Characteristics tissue: blood
cell type: PBMCs
strain: P.falciparum
age: 13
Extracted molecule total RNA
Extraction protocol PBMCs were isolated from whole blood via density centrifugation with Ficoll-Paque prior to cryopreservation. PBMC samples were thawed in RPMI 1640 (Gibco) containing 10% FCS and 0.02% Benzonase. 1E6 PBMCs were stained for viability with Propidium iodide (PI) and live cells were sorted on BD FACSAria™ III Cell Sorter into 2% FBS/PBS and counted on hemocytometer
Up to 10 000 cells were loaded into each lane of Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 and Gel Bead-in-Emulsion (GEMs) generated in Chromium Controller. 3’ Gene Expression Libraries were then generated according to manufacturer’s instructions. Generated libraries were sequenced in a NextSeq 550 System using High Output Kit (150 Cycles) with the following parameters read 1: 26 cycles, i7 index: 8 cycles, i5 index: 0 cycles, read 2: 98 cycles
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model NextSeq 550
 
Description 10x Genomics
Data processing Single cell sequencing data was demultiplexed, aligned and quantified using Cell Ranger software v6.0.1 (10x Genomics) against the human reference genome, with default parameters. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Quality control of the data, normalization, integration, clustering and sub-clustering was done using Seurat version 4.0.2.
Gene set enrichment analysis software was used to identify significantly enriched gene ontology terms
the HOMER v4.9 package was used to identify significantly overrepresented upstream regulators
Assembly: GRCh38 v 2.7.1a
Supplementary files format and content: Tab-separated values files and matrix files
 
Submission date Nov 14, 2022
Last update date Sep 27, 2023
Contact name Zuleima Pava Imitola
Organization name QIMR Berghofer
Street address 300 Herston road
City Brisbane
State/province Queensland
ZIP/Postal code 4006
Country Australia
 
Platform ID GPL21697
Series (1)
GSE217930 Malaria drives unique regulatory responses across multiple immune cells during human infection
Relations
BioSample SAMN31712599
SRA SRX18250200

Supplementary file Size Download File type/resource
GSM6730093_DEANO_barcodes.tsv.gz 16.3 Kb (ftp)(http) TSV
GSM6730093_DEANO_features.tsv.gz 170.6 Kb (ftp)(http) TSV
GSM6730093_DEANO_matrix.mtx.gz 14.3 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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