 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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 Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
