NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6523919 Query DataSets for GSM6523919
Status Public on Sep 02, 2022
Title Cartilage, Ossification, 45 day 1
Sample type SRA
 
Source name Cartilage
Organism Sus scrofa domesticus
Characteristics tissue: Cartilage
cell type: Primary cell
source: Chondrocytes and osteocytes
treatment: Osteogenesis of cartilage
Treatment protocol Cut up the tissue pieces on the ice, put the tissue into a mortar, add an appropriate amount of liquid nitrogen, grind quickly, and then add liquid nitrogen after the liquid nitrogen is reduced, grind it repeatedly for 3 times. The ground tissue fluid was used for the extraction of RNA
Extracted molecule total RNA
Extraction protocol The sample was extracted RNA by the RNA extraction Kit(RNeasy Mini Kit ,Cat#74106, Qiagen)
Magnetic beads were used to remove rRNA. Next, the RNA removed from rRNA was subjected to fragmentation, double-stranded cDNA synthesis, degradation of the second strand, end repair, addition of A to the 3 'end, junction and amplification experiments.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing The constructed library was used Qubit®2.0 Fluorometer to detect the concentration and Agilent2100 to detect the size.
The qualified library is sequenced by Illumina Novaseq 6000.
The original data are preprocessed to remove the joint sequence and low-quality reads. The data preprocessing software was used Seqtk.
Normalize the Fragments (trimmed mean of M values), and then calculate the FPKM value of each gene.
The preprocessed sequence was analyzed by genomic mapping using HISAT2 software.
Assembly: NCBI Sus_scrofa.Sscrofa10
 
Submission date Aug 30, 2022
Last update date Sep 02, 2022
Contact name lei xiang
E-mail(s) xljst1@sina.com
Organization name Jishuitan Hospital
Street address No. 31, Xinjiekou east street, Xicheng district
City BeiJing
ZIP/Postal code 100035
Country China
 
Platform ID GPL29562
Series (1)
GSE212315 Transcriptomic and proteomic studies of condylar ossification of the temporomandibular joint in porcine embryos
Relations
BioSample SAMN30594083
SRA SRX17321363

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap