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| Status |
Public on Jun 02, 2023 |
| Title |
P1-AR-day 7-1-CD45+ |
| Sample type |
SRA |
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| Source name |
heart
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| Organism |
Mus musculus |
| Characteristics |
tissue: heart
age: 8 days old
cell type: CD45+ cells
strain: C57BL/6
treatment: apical resection
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| Extracted molecule |
total RNA |
| Extraction protocol |
The heart tissues at day 7 after AR operated on postnatal day 1 (P1) and 7 (P7) mice were collected and minced into fine pieces. Tissues were enzymatically digested with a mixture of trypsin and collagenase. After dissociation, cell suspensions were passed through a 40 μm Cell Strainer, followed by red blood cells lysis. Then single cell suspensions were incubated with CD45 MicroBeads, mouse for 15 min at 4 °C, and isolated by a MACS Separator.
10× library preparation and sequencing Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation,so that each cell was paired with a bead in a Gel Beads-in emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 RevD). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific).
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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 Chromium X
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| Data processing |
Single cell RNA-seq data processing Reads were processed using the Cell Ranger 2.1.0 pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing output were aligned to the mouse genome, version GRCm38, using the STAR algorithm
We excluded cells with fewer than 200 or more than 6000 detected genes (where each gene had to have at least one UMI aligned in at least three cells). The expression of mitochondria genes was calculated using PercentageFeatureSet function of the seurat package.
To remove low activity cells, cells with more than 10 percent expression of mitochondria genes were excluded.
we performed principal component analysis (PCA) and reduced the data to the top 30 PCA components after scaled the data.
Identification of cell types and subtypes by nonlinear dimensional reduction (t-SNE) Cells were clustered using graph-based clustering of the PCA reduced data with the Louvain Method
Assembly: GRCm38
Supplementary files format and content: matrix table with raw gene counts for every gene and every cell
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| Submission date |
May 31, 2022 |
| Last update date |
Jun 02, 2023 |
| Contact name |
Zhenzhen Zhan |
| E-mail(s) |
zhanzz@tongji.edu.cn
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| Organization name |
Shanghai East Hospital, Tongji University School of Medicine,
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| Department |
Research Center for Translational Medicine
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| Street address |
Jimo Road 150
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| City |
Shanghai |
| ZIP/Postal code |
200120 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE205115 |
Murine neonatal cardiac B cells promote cardiomyocyte proliferation and heart regeneration |
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| Relations |
| BioSample |
SAMN28772807 |
| SRA |
SRX15503499 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6205410_P1-1_barcodes.tsv.gz |
109.2 Kb |
(ftp)(http) |
TSV |
| GSM6205410_P1-1_features.tsv.gz |
221.0 Kb |
(ftp)(http) |
TSV |
| GSM6205410_P1-1_matrix.mtx.gz |
138.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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