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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 14, 2024 |
| Title |
8 week mouse IVD [SM22-8W-1-1_S1] |
| Sample type |
SRA |
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| Source name |
whole IVD at the lumbar and the tail
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| Organism |
Mus musculus |
| Characteristics |
age: 8Wk
genotype: Tagln-CreERt2;R26tdTomato
tissue: whole IVD
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| Treatment protocol |
No special treatment was applied.
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| Growth protocol |
The mice grew under normal condition.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction from disassociated cells was done according to standard 10X Genomics Protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10X single-cell RNA-seq
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| Data processing |
Data was aligned to mouse genome mm10 (reference v3.0.0 provided by 10X Genomics) by CellRanger (version 3.1.0).
Data was also aligned to a reference file of exogenous sequences, including tdTomato (1431bp), by CellRanger (version 3.1.0).
The resulting matrix files were integrated and further processed on Seurat (version 3).
Dimension reduction including CCA, PCA, tSNE and UMAP were performed.
Clustering were performed, and differentially expressed genes between one cluster and another (or all remaining clusters) were performed. A further filtering of abs(log2(fold-change)) > 1/2 and FDR <0.05 was applied to ensure higher specificity and correct for multiple testing.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: gzip text files of gene expression.
Supplementary_files_format_and_content: P10_barcodes.tsv.gz: Gene expression file in mm10, for the p10 sample.
Supplementary_files_format_and_content: P10_features.tsv.gz: Gene expression file in mm10, for the p10 sample.
Supplementary_files_format_and_content: P10_matrix.mtx.gz: Gene expression file in mm10, for the p10 sample.
Supplementary_files_format_and_content: P10_exo_barcodes.tsv.gz: Gene expression file in exogenous genes, for the p10 sample.
Supplementary_files_format_and_content: P10_exo_features.tsv.gz: Gene expression file in exogenous genes, for the p10 sample.
Supplementary_files_format_and_content: P10_exo_matrix.mtx.gz: Gene expression file in exogenous genes, for the p10 sample.
Supplementary_files_format_and_content: 8W_barcodes.tsv.gz: Gene expression file in mm10, for the 8WK sample.
Supplementary_files_format_and_content: 8W_features.tsv.gz: Gene expression file in mm10, for the 8WK sample.
Supplementary_files_format_and_content: 8W_matrix.mtx.gz: Gene expression file in mm10, for the 8WK sample.
Supplementary_files_format_and_content: 8W_exo_barcodes.tsv.gz: Gene expression file in exogenous genes, for the 8WK sample.
Supplementary_files_format_and_content: 8W_exo_features.tsv.gz: Gene expression file in exogenous genes, for the 8WK sample.
Supplementary_files_format_and_content: 8W_exo_matrix.mtx.gz: Gene expression file in exogenous genes, for the 8WK sample.
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| Submission date |
Oct 25, 2021 |
| Last update date |
May 14, 2024 |
| Contact name |
Peikai Chen |
| E-mail(s) |
pkchen1@hku.hk
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| Phone |
852-258315217
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| Organization name |
The University of Hong Kong
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| Department |
Faculty of Medicine
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| Street address |
Sassoon Road 5
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| City |
Pok Fu Lam |
| ZIP/Postal code |
10000 |
| Country |
Hong Kong |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE186549 |
Tagln+ progenitors contribute to the development and maintenance of nucleus pulposus |
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| Relations |
| BioSample |
SAMN22562734 |
| SRA |
SRX12772253 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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