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Sample GSM7385144 Query DataSets for GSM7385144
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 The disc was retracted posteriorly and a periosteal elevator was placed under the disc to protect the condyle from secondary injury.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

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

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