GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM7981765

Query DataSets for GSM7981765

Status

Public on May 01, 2024

Title

synovium, msc_treat rep3

Sample type

SRA

Source name

synovium

Organism

Macaca fascicularis

Characteristics

tissue: synovium
treatment: Osteoarthritis model, msc treat
cell dose: 2.5*10e7

Extracted molecule

total RNA

Extraction protocol

Cartilage (~ 1 g) from intact and damaged regions of interest was minced finely with a sterile scalpel and collected in a 15 ml tube. A total of 15 ml of 0.4% Collagenase type II from Clostridium histolyticum (Sigma-Aldrich, Mo) made up in phosphate-bufered saline (PBS) and sterile filtered with a 0.22 μm filter, was added to the cartilage residua, incubated for 150 min at 37 °C rotating at 250 rpm. After enzymatic digestion, cells were pelleted by centrifugation, washed, sieved through a 30 μm cell strainer (Miltenyi Biotec, CA), pelleted by centrifugation again and resuspended in 1 ml PBS. Synovial membranes were dissected into small pieces, digested with 0.1% Collagenease Type IV from Clostridium histolyticum (Sigma-Aldrich, MO) in PBS for 1 h at 37 °C rotating at 250 rpm, then washed twice with PBS. Cells were centrifuged, washed, and sieved through a 30 μm cell strainer (Miltenyi Biotec, CA), pelleted by centrifugation again and resuspended in 1 ml PBS.
The GEMs(Gel Bead in Emulsion) were oil-treated, and the amplified cDNA was purified by magnetic beads, and then subjected to cDNA amplification and quality inspection. The 3ʹ Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation, adaptor ligation, sample index PCR, etc., the library is finally quantitatively examined. The final library pool was sequenced on the Illumina Novaseq6000 instrument using 150-base-pair paired-end reads.

Library strategy

RNA-Seq

Library source

transcriptomic single cell

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://www.10xgenomics.com/cn/support/software/cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

Submission date

Dec 19, 2023

Last update date

May 01, 2024

Contact name

Yan Yaping

E-mail(s)

[email protected]

Organization name

Macaca fascicularis

Department

Yunnan Key Laboratory of Primate Biomedical Research & Institute of Primate Translational Medicine