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| Status |
Public on Aug 14, 2022 |
| Title |
WT, scRNAseq |
| Sample type |
SRA |
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| Source name |
Heart
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| Organism |
Mus musculus |
| Characteristics |
cell type: cardaic nuclei
tissue: Heart
strain: C57BL/6
age: 6-month
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| Extracted molecule |
total RNA |
| Extraction protocol |
6-month old mice were used for snRNA-seq. Three hearts were pooled for each condition. Total cardaic nuclei were used to generate single-nucleus RNA-seq libraries.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, CD45+ immune cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The cDNA reads were aligned to the mm10/GRCm38 premRNA reference genome.
Further analyses for quality filtering was performed using the Seurat R package
For data quality filtering, we removed cells that had more than 6000 or fewer than 200 detected genes or cells that had a percent of mitochondrial genes > 10%.
We then normalized the data by the total expression, multiplied by a scale factor of 10,000 and log-transformed the result. IntegrateData function implemented in Seurat V4 was used to correct batch effects between samples and to merge samples into one Seurat object. Briefly, we performed standard preprocessing (log-normalization), and identified the top 2000 variable features for each individual dataset. We then identified integration anchors using the FindIntegrationAnchors function. We used default parameters and dimension 30 to find anchors. We then passed these anchors to the IntegrateData function to generate an integrated Seurat object
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Aug 11, 2022 |
| Last update date |
Aug 14, 2022 |
| Contact name |
Miao Cui |
| E-mail(s) |
[email protected]
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| Phone |
6263768016
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| Organization name |
UTSW
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| Street address |
UT Southwestern Medical Center Department of Molecular Biology 6000 Harry Hines Blvd.
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| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75390 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE211005 |
Precise genomic editing of a pathogenic RBM20 mutation rescues dilated cardiomyopathy |
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| Relations |
| BioSample |
SAMN30260393 |
| SRA |
SRX17028276 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6444327_WT_barcodes.tsv.gz |
47.4 Kb |
(ftp)(http) |
TSV |
| GSM6444327_WT_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM6444327_WT_matrix.mtx.gz |
59.7 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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