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| Status |
Public on Jul 02, 2024 |
| Title |
24 hours male CCI contralateral replicate 2 (same mouse as ipsilateral replicate 5) |
| Sample type |
SRA |
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| Source name |
3mm piece of Cortex & Hippocampus on the contralateral brain from the injury was cut- a mirror-image based on Allen-Brain atlas coordinates, then split into upper & lower quandrants, the upper quadrant was used.
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| Organism |
Mus musculus |
| Characteristics |
tissue: 3mm piece of Cortex & Hippocampus on the contralateral brain from the injury was cut- a mirror-image based on Allen-Brain atlas coordinates, then split into upper & lower quandrants, the upper quadrant was used.
cell type: Brain tissue
treatment: CCI
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| Growth protocol |
NA, Adult C57/BL6 male mice were used (litters aged 12-15 weeks, weighing 25-30 grams; Jackson Laboratories, ME, USA).
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| Extracted molecule |
total RNA |
| Extraction protocol |
3mm piece of Cortex & Hippocampus was cut, then split into upper & lower quandrants and the upper quadrant was placed into Collaganase IV Cocktail (10mg of DNAse, 32mg Collaganse IV, 20mg of Trypsin Soybean Inhibitor Worthington Chemicals), tissue was mechnically and enzymatically dissociated and strained into a single-cell suspension. Live cells were enriched in each sample, by removing the dead cells using Miltenyi Biotech dead cell removal kit, viability was determined and samples were loaded on a Next GEM G chip and placed into a 10x Genomics Chromium Controller
RNA libraries were prepared using Chromium Single Cell 3' Reagent Kits User Guide from 10x Genomics. Briefly, RNA was isolated and reverse transcibed into cDNA. The cDNA was then amplified and constructed into a 10x Genomics library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10X Genomics
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| Data processing |
We used 10X Cell Ranger 6.1.2 pipeline to perform the alignment to the reference genome, UMI demultiplexing, cell barcode identification, and subsequently generated the gene-cell expression matrices
We leveraged the Seurat based integrative analysis workflow for downstream analysis. Pre-processing includes merging the replicates, and quality control at the cell and gene level. Filter criteria was determined using the median number of genes using the quality control plots.
Additionally, we filtered out cells with a high fraction of reads mapping to the mitochondrial genome (>5%).
The multiplexed "CCI7" sample was aligned using the Cell Ranger "multi" pipeline to include cell-specific levels of antibody tags (HTOs). The 3 samples within the CCI7 dataset were demultiplexed using the "HTODemux" function and the abundance of the HTO from the Antibody Capture assay, with a classification threshold of 0.99.
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz - Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample.
Supplementary files format and content: barcodes.tsv.gz - Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample.
Supplementary files format and content: features.tsv.gz - Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene-count matrix for the respective sample.
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| Submission date |
Jun 13, 2024 |
| Last update date |
Jul 02, 2024 |
| Contact name |
Dhivyaa Rajasundaram |
| E-mail(s) |
dhr11@pitt.edu
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| Organization name |
University of Pittsburgh
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| Department |
Pediatrics
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| Street address |
4401 Penn Avenue
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| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15224 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE269748 |
A single-cell atlas deconstructs heterogeneity across multiple models in murine traumatic brain injury and identifies novel cell-specific targets |
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| Relations |
| BioSample |
SAMN41817269 |
| SRA |
SRX24911302 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8326347_RNASEQ18R_barcodes.tsv.gz |
48.2 Kb |
(ftp)(http) |
TSV |
| GSM8326347_RNASEQ18R_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM8326347_RNASEQ18R_matrix.mtx.gz |
70.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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