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| Status |
Public on Jul 25, 2018 |
| Title |
DTM-X_PBMC_live |
| Sample type |
SRA |
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| Source name |
whole blood
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| Organism |
Homo sapiens |
| Characteristics |
isolation: Ficoll
fixation: Live
resuspension: PBS
cell type: PBMC
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Human PBMCs were obtained from anonymous, healthy donors of the NIH Blood Bank. Cells were separated with LeucoSep tube filled with Ficoll-Paque-plus (GE Healthcare, Pittsburgh, PA) according to the manufacturer’s instruction. single-cell suspension was prepared following 10X Genomics Single cell protocols: Cell preparation guide (CG00053, Rev C).
Droplet-based single-cell partitioning and single-cell RNA-Seq libraries were generated using the Chromium Single-Cell 3′ Reagent v2 Kit (10X Genomics, Pleasanton, CA) as per the manufacturer’s protocol based on the 10X GemCode proprietary technology
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
cellranger version 2.0.1_mkfastq: bcl2fastq v1.9
cellranger version 2.0.1_count: The 98-bp-long read 2 containing the cDNA sequence was aligned using STAR against the GRCh38 human reference transcriptome. Unique molecular identifier (UMI) quantification, GemCode, and cell barcodes filtering based on error detection by Hamming distance were performed as described by Zheng et al
cellranger version 2.0.1_aggr: It normalizes multiple runs to the same sequencing depth (default=mapped) and then re-computes and produces a new single gene-barcode matrix containing all the data for correlation analysis.
Loupe™ Cell Browser (v2.0) was used to view the entire dataset and interactively find significant genes, cell types, and substructure within cell clusters.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files with filtered_gene_bc_matrices
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| Submission date |
Apr 09, 2018 |
| Last update date |
Jul 25, 2018 |
| Contact name |
Jinguo Chen |
| E-mail(s) |
[email protected]
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| Phone |
2406273273
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| Organization name |
NIH
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| Department |
NIAID
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| Lab |
Center for Human Immunology (CHI)
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| Street address |
10 Center Drive
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE112845 |
PBMC Fixation and Processing for Chromium Single-Cell RNA Sequencing |
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| Relations |
| BioSample |
SAMN08893676 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3087619_DTM-X_PBMC_live_barcodes.tsv.gz |
20.1 Kb |
(ftp)(http) |
TSV |
| GSM3087619_DTM-X_PBMC_live_genes.tsv.gz |
258.6 Kb |
(ftp)(http) |
TSV |
| GSM3087619_DTM-X_PBMC_live_matrix.mtx.gz |
19.0 Mb |
(ftp)(http) |
MTX |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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