|
| Status |
Public on May 25, 2023 |
| Title |
Osteoarthritis, Superficial zone cells, Biol rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
Temporomandibular Joint
|
| Organism |
Oryctolagus cuniculus |
| Characteristics |
tissue: Temporomandibular Joint
cell type: Superficial zone cells
genotype: WT
disease state: Osteoarthritis
|
| Treatment protocol |
Temporomandibular joint osteoarthritis was surgically induced using a disc perforation model. An incision was created superior to the zygomatic process. The disc was retracted posteriorly and a periosteal elevator was placed under the disc to protect the condyle from secondary injury. A punch biopsy was used to create a 2.5 mm in the posterior-lateral TMJ disc and the perforated disc tissue was removed. No disc attachments were severed and the disc reduced to its normal anatomical location.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from tissue samples using RNeasy Micro kit (Qiagen).
QIAseq FastSelect rRNA HMR Kit (Qiagen) was used for rRNA depletion, followed by library preparation using NEBNext Ultra II Directional RNA Library Prep Kit (NEB).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
RPFC_3
|
| Data processing |
MultiQC (1.13) for quality check. Trim Galore (0.6.7) for adapter and quality trimming.
First time read alignment with STAR (2.7.9a) with parameters of: --chimSegmentMin 10 --alignEndsType Local --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 70 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMstrandField intronMotif --outFilterType BySJout --twopassMode Basic.
Mapping restuls from the first time read alignment then passed to StringTie (2.1.0) for reference-based (OryCun2.0 Eensembl release-105) de novo transcriptome assembly with parameters of: -m 100 -a 5 -j 0.1 -c 0.5 -f 0.005
Finally, trimmed sequence reads were mapped to de novo transcriptome assembly using Salmon software (1.1.0).
The estimated TPM and read counts from Salmon software was converted to gene-level following the DESeq2 (1.26.0) manual.
Assembly: OryCun2.0
Supplementary files format and content: excel file include TPM and read counts for each sample
|
| |
|
| Submission date |
May 19, 2023 |
| Last update date |
May 25, 2023 |
| Contact name |
Ikue Tosa |
| E-mail(s) |
it2318@cumc.columbia.edu
|
| Organization name |
Columbia University
|
| Department |
College of Dental Medicine
|
| Lab |
Embree Lab
|
| Street address |
P&S 16-440 630 W. 168th St.
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL25392 |
| Series (1) |
| GSE232867 |
Bulk RNA-seq analyses of mandibular condylar cartilage in a post-traumatic temporomandibular joint osteoarthritis rabbit model |
|
| Relations |
| BioSample |
SAMN35177625 |
| SRA |
SRX20435566 |
