|
| Status |
Public on Oct 31, 2024 |
| Title |
KO_gingiva infiltration immune cells |
| Sample type |
SRA |
| |
|
| Source name |
murine gingiva infiltration immune cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Otud1-/-
tissue: gingiva
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The Cell ranger software pipeline (version 5.0.0) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 3.2.3) was used for generation of Seurat object.
Low-quality cells with UMI numbers greater than 3000 or less than 300, or having over 10% mitochondrial-derived UMI counts were removed.
The count matrix was normalized with SCTransform function.
IntegrateData function was used to integrate data and create a new matrix with 3000 features.
PCA was performed by R package Seurat (version 3.2.3). Top 50 PCs were used for tSNE and UMAP.
tSNE and UMAP were performed by R package Seurat (version 3.2.3).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.
|
| |
|
| Submission date |
Oct 25, 2022 |
| Last update date |
Oct 31, 2024 |
| Contact name |
Jia Song |
| E-mail(s) |
songjia@bjmu.edu.cn
|
| Phone |
+18830053918
|
| Organization name |
Peking University
|
| Street address |
Peking University School of Medicine, 38 Xueyuan Road, Haidian District, Beijing
|
| City |
Beijing |
| State/province |
China |
| ZIP/Postal code |
100080 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE216573 |
The deubiquitinase OTUD1 attenuates periodontal inflammation by restricting neutrophil protein transport |
|
| Relations |
| BioSample |
SAMN31445433 |
| SRA |
SRX18025336 |
