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Sample GSM5813911

Query DataSets for GSM5813911

Status

Public on Jul 31, 2023

Title

Healthy mouse 1

Sample type

SRA

Source name

Joint_Healthy_mouse

Organism

Mus musculus

Characteristics

strain: 129/Sve
age: 8 weeks old
Sex: female
disease: Healthy
tissue: Joint

Treatment protocol

After pre-sensitization to mBSA, antigen induced arthritis (AIA) was triggered in 8 weeks old, female mice. The healthy control mice were injected with phosphate-buffered saline. One week after triggering, the mice were sacrificed. Successful AIA was ensured among the sick mice by immunohistochemistry, and whole joints were prepared for scRNA-seq using the Seq-Well method. To increase read coverage, each sample was sequenced multiple times.

Extracted molecule

polyA RNA

Extraction protocol

The bam files were extracted following all the steps of James Nemesh, McCarrol’s lab Drop-seq Core Computational Protocol (version 1.0.1) (http://mccarrolllab.com), using bcl2fastq conversion and Picard software. The fastq files from the same sample (multiple sequencing rounds) were merged after bcl2fastq extraction.
Libraries were prepared from GRCh38 (April 2017, Ensembl) using STAR software.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Data processing

Processed of scRNA-seq data into digital gene expression matrices following James Nemesh, McCarrol’s lab Drop-seq Core Computational Protocol (version 1.0.1) (http://mccarrolllab.com) using bcl2fastq conversion and Picard software. The indexed reference for alignment of the reads was generated from GRCm38 (June 2017, Ensembl) using STAR software. NCBI Gene Symbols were used for annotation.
Quality control, where cells with less than 10,000 reads, 400 transcripts, or 200 genes, or more than 20% mitochondrial genes were sorted out.
Genes expressed in less than three cells were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with transcript counts of each gene (rows) within each cell (columns).

Submission date

Jan 12, 2022

Last update date

Jul 31, 2023

Contact name

Sandra Lilja

Organization name

Linköping University

Department

BKV

Street address

Sandbäcksgatan 7