|
| Status |
Public on Jan 19, 2019 |
| Title |
s05 |
| Sample type |
SRA |
| |
|
| Source name |
dissected spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
Sex: male
age: 6 weeks
cell type: singlet/live/CD45+
serum injected: C57BL/6J mouse serum
treatment: sham
|
| Treatment protocol |
ultrasound treatment parameters: 1 MHz ultrasound at 350 kPa using 1s on/5s off bursts for a total of 12 minutes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
extraction occurs similtaneously with library prep on a cell-by-cell basis
10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit (v2) per manufactures instructions
All samples pooled and sequenced on 2 lanes of Illumina NovaSeq 6000 Sequencer
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
s05 control mouse, sham treatment
|
| Data processing |
Basecalling performed by NovaSeq 6000 software RTA3
Reads aligned to mm10 genome using Cell Ranger 2.1.0 using STAR 2.5.1b
Data was filtered: genes in detected in >0.1% cells per sample, and cells with detected genes >200 and <3000, <0.075 mitochondrial genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include filtered, normalized and scaled count values for each cell (UMI) in each sample
|
| |
|
| Submission date |
Jan 18, 2019 |
| Last update date |
Jan 20, 2019 |
| Contact name |
Rachel Stegeman Graham |
| E-mail(s) |
rgraham@umn.edu
|
| Phone |
7632277202
|
| Organization name |
University of Minnesota
|
| Department |
Pediatrics
|
| Lab |
Binstadt
|
| Street address |
2101 6th St SE
|
| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55414 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE125316 |
Noninvasive ultrasound stimulation of the spleen to treat inflammatory arthritis - single cell RNA sequencing of splenic leukocytes |
|
| Relations |
| BioSample |
SAMN10769617 |
| SRA |
SRX5263701 |
