|
| Status |
Public on Sep 28, 2022 |
| Title |
Periodontal ligament tissue periodontitis |
| Sample type |
SRA |
| |
|
| Source name |
Periodontal ligament tissue periodontitis
|
| Organism |
Mus musculus |
| Characteristics |
diagnosis: periodontitis
strain: CD1
tissue: periodontal ligament
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tooth were extracted and digested with collagenase P. Single cells suspensions were fed into 10X Chromium.
Library was generated with Chromium Single Cell 3' v3 Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Count matrices were generated from the fastq files via CellRanger pipeline using Ensembl 97 genome annotation.
Ambient and background RNA from the count matrices were first removed using CellBender remove‐background tool.
Only cells expressing >1000 features and having mitochondria gene content of less than 5% of total cell content were maintained.
Batch effect was removed by Seurat CCA approach. Integrated data were subsequently scaled and PCA was performed, followed by UMAP for embedding and Louvain clustering on knn graph.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: PTIS.TXT: Processed raw count matrix.
|
| |
|
| Submission date |
Feb 28, 2021 |
| Last update date |
Sep 28, 2022 |
| Contact name |
Paul Sharpe |
| Organization name |
King's college London
|
| Street address |
Craniofacial Development & Stem cell bio, Guy's Tower Floor 27
|
| City |
london |
| ZIP/Postal code |
SE1 9RT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE167917 |
Telocytes regulate tissue resident macrophages in periodontal disease |
|
| Relations |
| BioSample |
SAMN18090453 |
| SRA |
SRX10191228 |
