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| Status |
Public on Sep 27, 2023 |
| Title |
Child3_Day7 |
| Sample type |
SRA |
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| Source name |
blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
cell type: PBMCs
strain: P.falciparum
age: 13
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Description |
10x Genomics
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| 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
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| Submission date |
Nov 14, 2022 |
| Last update date |
Sep 27, 2023 |
| Contact name |
Zuleima Pava Imitola |
| Organization name |
QIMR Berghofer
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| Street address |
300 Herston road
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| City |
Brisbane |
| State/province |
Queensland |
| ZIP/Postal code |
4006 |
| Country |
Australia |
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| Platform ID |
GPL21697 |
| Series (1) |
| GSE217930 |
Malaria drives unique regulatory responses across multiple immune cells during human infection |
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| Relations |
| BioSample |
SAMN31712604 |
| SRA |
SRX18250205 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6730098_DEANT_barcodes.tsv.gz |
30.1 Kb |
(ftp)(http) |
TSV |
| GSM6730098_DEANT_features.tsv.gz |
170.6 Kb |
(ftp)(http) |
TSV |
| GSM6730098_DEANT_matrix.mtx.gz |
33.1 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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