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| Status |
Public on Sep 15, 2022 |
| Title |
MGT_scATAC |
| Sample type |
SRA |
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| Source name |
cardiac
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: heart
age: 1-3 days
genotype: wild type
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| Treatment protocol |
For direct cardiac reprogramming, pMXs retrovirus encoding Mef2c, Gata4, Tbx5, and Ascl1 were packaged by transfecting platE cells with Trans-IT as the manufacturer suggested. Viruses were collected from one 10-cm dish were resuspended in 100μl iCM medium(400ml DMEM, 100ml M199, and 50ml FBS). All virus transductions were performed in the iCM medium containing 4 μg/ml of polybrene. For single-cell multiomics, cardiac fibroblasts were transduced with M, G, and T viruses for MGT induced reprogramming sample or equal amounts of M and A for AM induced reprogramming sample.
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| Growth protocol |
Mice were raised and maintained under standard laboratory conditions.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested by trypsin and nuclei were harvested using 10x provided protocol.
Illumina libraries were prepared usingSingle Cell Multiome ATAC + Gene Expression kit.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Raw sequencing data was demultiplexed, debarcoded, mapped to Cell Ranger pre-built mm10 genome, and counted following the Cell Ranger ARC pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R using seurat.
Genome_build: Cell Ranger pre-built mm10 reference
Supplementary_files_format_and_content: Two csv files containing peak count for cells in the two samples, respectively
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| Submission date |
Dec 29, 2021 |
| Last update date |
Sep 15, 2022 |
| Contact name |
LI QIAN |
| E-mail(s) |
li_qian@med.unc.edu
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| Phone |
919 9624982
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| Organization name |
UNC
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| Department |
Department of pathology
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| Lab |
Qian Lab
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| Street address |
111 Mason Farm Road, MBRB
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| City |
Chapel Hill |
| ZIP/Postal code |
27517 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE192738 |
Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [scATAC-seq] |
| GSE192788 |
Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes |
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| Relations |
| BioSample |
SAMN24495394 |
| SRA |
SRX13549156 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5764241_MGT_ATAC_count_matrix.csv.gz |
74.3 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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