|
| Status |
Public on Mar 06, 2023 |
| Title |
acATAC_KI_1 |
| Sample type |
SRA |
| |
|
| Source name |
heart
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N
day: embryonic day 17.5
genotype: Q353R
name in supplementary file: KI_1
|
| 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).)
|
| 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.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryonic hearts of E17.5 were minced and enzymatically dissociated using the same digestion buffer as what used in the scRNA-seq analysis.
scATAC-seq targeting 3,000 cells per sample was performed using Chromium Single Cell ATAC Library and Gel Bead 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).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
scATAC-seq
|
| 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
|
| |
|
| 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
|
| Phone |
81338155411
|
| Organization name |
The University of Tokyo
|
| Department |
Department of Cardiovascular Medicine
|
| Street address |
7-3-1, Hongo, Bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
113-8655 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE190977 |
TEAD1 trapping by the Q353R-Lamin A/C causes dilated cardiomyopathy. |
|
| Relations |
| BioSample |
SAMN24103328 |
| SRA |
SRX13417291 |
