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Status |
Public on Oct 02, 2024 |
Title |
Donor2_ADT |
Sample type |
SRA |
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Source name |
Peripheral blood
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Organism |
Homo sapiens |
Characteristics |
tissue: Peripheral blood cell type: CD14- CD19- CD45+ 5-OP-RU-hMR1-tetramer+/-
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Extracted molecule |
protein |
Extraction protocol |
Peripheral blood was obtained from four healthy human donors. After lymphocyte isolation, 5-OP-RU-hMR1-tetramer-PE-positive cells were magnetically enriched and marked (HTO#1). 5-OP-RU-hMR1-tetramer-PE-negative cells were counter-stained (HTO#3). Both populations were stained with CITE-seq antibodies and sorted as live CD14- CD19- CD45+ MAITcells (5OPRU-hMR1-tetramer-positive) and non-MAIT cells (5-OPRU-hMR1-tetramer-negative). Single cell libraries were created following the 10X Chromium Next GEM Single Cell 5' v2 protocols with feature barcode technology for cell surface protein and immune receptor mapping. Libraries were pooled and sequenced with a 26-10-10-90 nucleotide read setup on a Illumina NovaSeq6000 v1.5 S1-100 at the National Genomics Infrastructure at the Science for Life Laborartory in Stockholm, Sweden.
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Library strategy |
OTHER |
Library source |
other |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
ADT
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Data processing |
BCL to FASTQ conversion was performed using CASAVA software's bcl2fastq_v2.20.0.422. Sequence alignment was performed following the cellranger multi pipeline (v6.1.2). Singlets were identified using HTODemux (Stoeckius et al., DOI: 10.1186/s13059-018-1603-1) and scDblFinder (Germain et al., DOI: 10.12688/f1000research.73600.2). Cells were quality controlled (nFeature_RNA>200, nCount_RNA>1000, nCount_RNA<8000, percent_mito<10, percent_ribo>10). Cells annotated as T cells or NK cells by sc-type algorithm were retained for downstream analysis. Assembly: GRCh38-2020-A Library strategy: CITE/TCR-seq
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Submission date |
Nov 08, 2023 |
Last update date |
Oct 02, 2024 |
Contact name |
Johan K. Sandberg |
Organization name |
Karolinska Institutet
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Department |
Department of Medicine Huddinge
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Lab |
Center for Infectious Medicine
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Street address |
Alfred Nobels Allé 8b
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City |
Huddinge |
State/province |
Stockholms |
ZIP/Postal code |
14152 |
Country |
Sweden |
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Platform ID |
GPL24676 |
Series (1) |
GSE247338 |
Characterization of human CD56+ MAIT cells in peripheral blood |
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Supplementary file |
Size |
Download |
File type/resource |
GSM7887370_Donor2_ADT_Kammann_et_al.rds.gz |
185.8 Kb |
(ftp)(http) |
RDS |
Raw data not provided for this record |
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