|
| Status |
Public on May 05, 2024 |
| Title |
snRNA_lung_wt |
| Sample type |
SRA |
| |
|
| Source name |
lung tissue from E18.5 mouse embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung tissue from E18.5 mouse embryo
genotype: wild type
strain background: C57BL/6
|
| Treatment protocol |
CTCF-R567W mutation were generated by CRISPR/Cas9-mediated genome editing.
|
| Growth protocol |
Mice were housed in a specific pathogen–free (SPF) facility with a 12 h dark/12 h light cycle and provided with food and water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SnRNA-seq experiments for E18.5 heart and lung tissues were performed by Jiayin Biotechnology Ltd.
Libraries were constructed according to instruction manual of the Chromium Single Cell 3’ Reagent Kits v3 with 10 x Genomics platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
library strategy: snRNA-seq
For snRNA-seq data analysis, paired-end reads were aligned to mouse reference genome (mm10) using Cell Ranger.
Raw count matrices were used to remove ambient RNA with SoupX, then analyzed using Seurat. Poor quality cells were filtered out. Potential doublets were removed with DoubletFinder.
The data was then normalized and integrated using SCTransform integration workflow by regressing out cell cycle effect and percentages of mitochondria-expressed genes per cell. Principal component analysis (PCA) was performed, dimensionality reduction (UMAP) and clustering were then carried out. Cell markers for each cell cluster were determined with FindAllMarkers function.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Oct 03, 2022 |
| Last update date |
May 05, 2024 |
| Contact name |
gongcheng Hu |
| Organization name |
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences
|
| Street address |
190 Kai Yuan Avenue, Science Park, Guangzhou, China
|
| City |
guangzhou |
| State/province |
guangdong |
| ZIP/Postal code |
510530 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE214690 |
Dissecting developmental disorders caused by CTCF mutation at R567 [snRNA-seq] |
| GSE214692 |
Dissecting developmental disorders caused by CTCF mutation at R567 |
|
| Relations |
| BioSample |
SAMN31138603 |
| SRA |
SRX17781808 |
