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Sample GSM7887370 Query DataSets for GSM7887370
Status Public on Oct 02, 2024
Title Donor2_ADT
Sample type SRA
 
Source name Peripheral blood
Organism Homo sapiens
Characteristics tissue: Peripheral blood
cell type: CD14- CD19- CD45+ 5-OP-RU-hMR1-tetramer+/-
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.
 
Library strategy OTHER
Library source other
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description ADT
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
 
Submission date Nov 08, 2023
Last update date Oct 02, 2024
Contact name Johan K. Sandberg
Organization name Karolinska Institutet
Department Department of Medicine Huddinge
Lab Center for Infectious Medicine
Street address Alfred Nobels Allé 8b
City Huddinge
State/province Stockholms
ZIP/Postal code 14152
Country Sweden
 
Platform ID GPL24676
Series (1)
GSE247338 Characterization of human CD56+ MAIT cells in peripheral blood

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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