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Sample GSM3568835 Query DataSets for GSM3568835
Status Public on Jan 19, 2019
Title s16
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: K/B.g7 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 s16 arthritic 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
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
BioSample SAMN10769606
SRA SRX5263712

Supplementary file Size Download File type/resource
GSM3568835_s16_processeddata.txt.gz 158.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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