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| Status |
Public on Mar 06, 2023 |
| Title |
scRNA_E17.5_WT_1 |
| Sample type |
SRA |
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| Source name |
heart
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N
day: embryonic day 17.5
genotype: WT
name in supplementary file: E17.5_WT_1
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| Treatment protocol |
Lmna Q353R knock-in mice were generated as previously described (Hara, S. et al. Generation of mutant mice via the CRISPR/Cas9 system using FokI-dCas9. Sci. Rep. 5, 1–9 (2015).)
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| Growth protocol |
All the animal experiments were approved by the University of Tokyo Ethics Committee for Animal Experiments and strictly adhered to the guidelines for animal experiments of the University of Tokyo (Approved Number P17-058). All mice were housed in separate cages at a maximum of 6 mice per cage in a specific-pathogen–free, temperature-controlled vivarium under a 12-h light/dark cycle with ad libitum access to food and water.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Embryonic hearts of E13.5 and E17.5 were minced and enzymatically dissociated using 2 mg/mL type 2 collagenase, 1 mg/mL dispase, and 20 U/mL DNase I, with 5 cycles of digestion for a total 40 min at 37 °C. After using a 40-μm cell strainer to remove the debris and multiplets, 5,000 cells were prepared to a concentration of 1000 cells/µL and loaded into the Chromium Controller.
single-cell cDNA libraries were generated using the Chromium 3’ v3 chemistry kit (10x Genomics) according to the manufacturer’s instruction. Libraries were sequenced on a NovaSeq 6000 System (Illumina) using a NovaSeq S4 Reagent Kit (200 cycles, 20027466, Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
scRNA-seq
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| Data processing |
Cell Ranger software (ver 3.0.2, 10X Genomics)
Cell Ranger ATAC software (ver 1.2.0, 10X Genomics)
Genome_build: Cell Ranger mm10 reference genome
Supplementary_files_format_and_content: tsv files and mtx files from Cell Ranger and h5 files from Cell Ranger ATAC
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| Submission date |
Dec 15, 2021 |
| Last update date |
Mar 08, 2023 |
| Contact name |
Shintaro Yamada |
| E-mail(s) |
shintayamada-tky@g.ecc.u-tokyo.ac.jp
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| Phone |
81338155411
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| Organization name |
The University of Tokyo
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| Department |
Department of Cardiovascular Medicine
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| Street address |
7-3-1, Hongo, Bunkyo-ku
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| City |
Tokyo |
| ZIP/Postal code |
113-8655 |
| Country |
Japan |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE190977 |
TEAD1 trapping by the Q353R-Lamin A/C causes dilated cardiomyopathy. |
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| Relations |
| BioSample |
SAMN24103329 |
| SRA |
SRX13417290 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5736796_E17.5_WT_1_barcodes.tsv.gz |
106.4 Kb |
(ftp)(http) |
TSV |
| GSM5736796_E17.5_WT_1_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM5736796_E17.5_WT_1_matrix.mtx.gz |
88.4 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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