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Sample GSM4110027 Query DataSets for GSM4110027
Status Public on Oct 07, 2019
Title HLH_T2_scRNAseq
Sample type SRA
 
Source name Peripheral blood mononuclear cell
Organism Homo sapiens
Characteristics tissue: PBMC
treatment time: Day 7, T1
disease state: EBV-HLH
Extracted molecule polyA RNA
Extraction protocol Preparation: Collect 3ml herprized peripheral blood from patient. Put all regent, 1×ACK, 0.04% PBS-BSA, and sample on ice;Lyse RBCs;Centrifuge at 300g, RT for 3min;Collect the plasma (around 1.5ml) in an EP tube;Add 30ml 1×ACK to resuspend blood by inverting the tube;Put the mixed ACK-sample on ice and lysis for <7min (keep inverting the tube during lysis);Centrifuge at 300g, RT for 3min;Discard the supernatant;Add 10ml 1×ACK to lysis again;Lysis on ice for <5min (keep inverting the tube during lysis);Centrifuge at 300g, RT for 3min;Discard the supernatant.;Wash and count (get rid of dead cells);Resuspend cells by 5ml 0.04% PBS-BSA pre-cold buffer;Mix throughout by pipetting;Suck out 10ul for counting (add 10ul Typan Blue);Suck out 2×106 cells into EP tube and put the remaining cells on ice;Centrifuge the EP tube at 100g, RT for 3min;Discard the supernatant;Resuspend the cells using 1ml 0.04%PBS-BSA buffer;Centrifuge at 100g, RT for 3min;Discard the supernatant;Resuspend the cells using 830ul 0.04%PBS-BSA buffer;Count (both living and dead cells) twice;Keep the density of living cells between 0.7~1.2×106/ml;Freeze the remaining cells
Follwed by v2 protocol of chemistry of the 3’ scRNA-seq 10X genomics platform
single cell RNA-seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing ScRNA-seq alignment process was completed by cellranger(version 3.0.0)
Seurat V3 workflow
Genome_build: hg19 human genome references
Supplementary_files_format_and_content: txt files with gene counts
 
Submission date Oct 07, 2019
Last update date Oct 09, 2019
Contact name Xaingyu Pan
E-mail(s) pangxueyu233@outlook.com
Organization name Sichuan University
Department State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.
Lab Chen & Liu Lab
Street address No.17 Renming road section3
City Chengdu, Cihna
State/province Sichuan
ZIP/Postal code 610041
Country China
 
Platform ID GPL24676
Series (1)
GSE138504 Nivolumab treatment for relapsed/refractory Epstein-Barr virus-associated hemophagocytic lymphohistocytosis in adults
Relations
BioSample SAMN12982837
SRA SRX6957863

Supplementary file Size Download File type/resource
GSM4110027_HLH_T2_counts.txt.gz 4.8 Mb (ftp)(http) TXT
GSM4110027_anno_HLH_T2.rds.gz 289.0 Mb (ftp)(http) RDS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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