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Status |
Public on Jan 26, 2023 |
Title |
co-culture-rep1 |
Sample type |
SRA |
|
|
Source name |
mouse cardiac fibroblast
|
Organism |
Mus musculus |
Characteristics |
tissue: mouse heart ventricle condition: 3D culture in GelMA system cell type: cardiac fibroblast co-cultured with endothelial cell
|
Treatment protocol |
Cardiac fibroblasts were cultured alone or co-cultured with endothelial cells for 7 days in 5% 3D GelMa system (EFL, EFL-GM-90).
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Growth protocol |
Mouse cardiac fibroblasts were isolated from mouse heart ventricles and cultured in low-glucose DMEM media (Corning, 10-014-CV) supplemented with 10% FBS (Gibco, 10270-106), 10 μM ROCK inhibitor (MedExpress, HY-15720) and 1% penicillin/streptomycin (Thermo). Mouse endothelial cells were isolated from mouse heart and lung and cultured in dishes pre-coated with 1% fibronectin with EGM-2 MV media (Lonza, CC-3202).
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Cardiac fibroblasts cultured alone were extracted directly from 3D GelMA dissosiation, cardiac fibroblasts (CD45-CD31-Pdgfr-α+) co-cultured with endothelial cells were flow cytometrically sorted from 3D GelMA co-culture system. RNA-seq libraries were constructed by a modified Smart-seq2 method with UMI barcodes (Nature 533:487, 2016).
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|
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 mouse genome using STAR. For RNA-seq data, aligned reads with high quality were quantified by HTSeq. For RNA-seq data, counts per million reads (CPM) were calculated. For RNA-seq data, unique molecular identifiers (UMIs) were extracted from Read2. Raw gene counts were calculated by UMI number to get rmdup.count file. Genome_build: mm10 Supplementary_files_format_and_content: We provided tab-delimited text files including raw count values for each sample.
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|
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Submission date |
Sep 29, 2021 |
Last update date |
Jan 28, 2023 |
Contact name |
Dandan Cao |
E-mail(s) |
1931465@tongji.edu.cn
|
Phone |
17853136996
|
Organization name |
Tongji University
|
Street address |
1239 Siping Road, Yangpu District
|
City |
Shanghai |
ZIP/Postal code |
200092 |
Country |
China |
|
|
Platform ID |
GPL24247 |
Series (1) |
GSE184986 |
Inhibition of Fap Promotes Cardiac Repair by Stabilizing BNP |
|
Relations |
BioSample |
SAMN21897514 |
SRA |
SRX12403062 |