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| Status |
Public on Oct 07, 2019 |
| Title |
HLH_T4_scRNAseq |
| Sample type |
SRA |
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| Source name |
Peripheral blood mononuclear cell
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| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMC
treatment time: Day 76, T3
disease state: EBV-HLH
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Oct 07, 2019 |
| Last update date |
Oct 09, 2019 |
| Contact name |
Xaingyu Pan |
| E-mail(s) |
[email protected]
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| Organization name |
Sichuan University
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| Department |
State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.
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| Lab |
Chen & Liu Lab
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| Street address |
No.17 Renming road section3
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| City |
Chengdu, Cihna |
| State/province |
Sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE138504 |
Nivolumab treatment for relapsed/refractory Epstein-Barr virus-associated hemophagocytic lymphohistocytosis in adults |
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| Relations |
| BioSample |
SAMN12982835 |
| SRA |
SRX6957865 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4110029_HLH_T4_counts.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSM4110029_anno_HLH_T4.rds.gz |
127.1 Mb |
(ftp)(http) |
RDS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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