|
| Status |
Public on Nov 10, 2019 |
| Title |
flare1-1 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: PBMCs
condition: SLE flare
sample type: primary cells
chip antibody: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PBMCs from SLE patients and healthy controls were Ficoll-isolated and prepared using the 10x Chromium Single cell instrument standard protocol.
10x Chromium Single Cell Workflow
10x Chromium Single Cell Library Prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
flare.mtx
|
| Data processing |
10x CellRanger was run on each faw sample with default settings
Demuxlet software was run on each sample with default settings and genotyping parameter 0.1
Counts matrices from the 10x Cellranger software were aggregated across samples and doublets flagged by Demuxlet were removed
Genome_build: hg19
Supplementary_files_format_and_content: MTX files (count matrices), TXT files (row and column annotations)
|
| |
|
| Submission date |
Sep 06, 2019 |
| Last update date |
Nov 10, 2019 |
| Contact name |
Meena Subramaniam |
| E-mail(s) |
meena.s.subramaniam@gmail.com
|
| Organization name |
UCSF IHG
|
| Street address |
513 Parnassus Ave S-965
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE137029 |
Multiplexed RNA-sequencing of 1M immune cells reveals the cellular, molecular, and genetic correlates of systemic lupus erythematosus |
|
| Relations |
| BioSample |
SAMN12709122 |
| SRA |
SRX6813329 |
