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Sample GSM5602740 Query DataSets for GSM5602740
Status Public on Jan 26, 2023
Title co-culture-rep3
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).
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).
 
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.
 
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 SAMN21897516
SRA SRX12403064

Supplementary file Size Download File type/resource
GSM5602740_SYX-3_L4_A002.rmdup.count.txt.gz 196.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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