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| Status |
Public on Apr 20, 2020 |
| Title |
m_NCM_AF1 |
| Sample type |
SRA |
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| Source name |
cardiomyocytes
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
co-cultured cell type: adult fibroblasts
cell type: cardiomyocytes
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cell suspension was centrifuge (100 x g, 2min) three times to separate the cardiomyocytes and non-cardiomyocytes
RNA was extracted from cells using the GeneJet RNA Purification Kit (Thermo Scientific). One µg of RNA was used for generation of sequencing library using the TruSeq RNA Library Prep Kit V2 (Illumina) according to the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
RNAseq_genecountsraw.txt
RNAseq_logFC_cafNCMmcnfNCM.xlsx
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| Data processing |
Raw reads were filtered by cutadpt v1.8.1,-m 20 --trim-n --max-n 0.7 -q 20
Contaminants were filtered by fastq_screen (v0.5.1. 4)
Clean reads were mapped to UCSC mm10 genome via STAR v2.5.2b
Reads were assigned to Ensembl genes by featureCounts (subread-1.4.6-p1 command line)
Genome_build: mm10
Supplementary_files_format_and_content: csv,gene expression matrix for single cell RNASeq
Supplementary_files_format_and_content: txt,raw counts of RNA-seq
Supplementary_files_format_and_content: xlsx,log fold change of RNA-seq
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| Submission date |
Dec 10, 2018 |
| Last update date |
Apr 20, 2020 |
| Contact name |
Li Wang |
| Organization name |
NIH
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| Street address |
111 T.W. Alexander Dr
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| City |
Durham |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE123547 |
A critical role of fibroblast in cardiac maturation as revealed by single-cell RNA-Sequencing |
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| Relations |
| BioSample |
SAMN10564375 |
| SRA |
SRX5123303 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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