|
Status |
Public on Jan 19, 2019 |
Title |
s15 |
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: ultrasound
|
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 |
s15 control mouse, ultrasound 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 |
SAMN10769607 |
SRA |
SRX5263711 |