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| Status |
Public on Jun 06, 2024 |
| Title |
KO3, E18.5, heart |
| Sample type |
SRA |
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| Source name |
heart
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| Organism |
Mus musculus |
| Characteristics |
tissue: heart
genotype: C10orf71 KO
age: E18.5
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| Extracted molecule |
total RNA |
| Extraction protocol |
For embryonic mice, hearts were isolated from E18.5 embryos generated by heterozygous parents and stored in Trizol reagent prior to genotyping. Three hearts per genotype were pooled together and total RNA was extracted. RNA quality was evaluated via the Lab-Chip technique (Agilent Bioanalyzer). For adult mice, we extracted total RNA from hearts using Trizol.
The libraries were constructed using NEBNext® UltraTM RNA Library Prep Kit for Illumina®
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
KO3
E18.5.txt
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| Data processing |
Relative expression (fragments per kilobase per million mapped reads, FPKM) was calculated using uniquely mapped pairs with Cufflinks software (Version 2.2.1).
Down-regulated differentially expressed genes (DEGs) from KO embryonic heart met the following criteria: 1) average FPKM in WT group > 2; 2) p-value < 0.1; 3) fold change (mutant/WT) < 0.8. Up-regulated DEGs met the following criteria: 1) average FPKM in KO group > 2; 2) p-value < 0.1; 3) fold change (mutant/WT) > 1.2.
Down-regulated DEGs from KO adult heart satisfied the following criteria: 1) average FPKM in WT group > 2; 2) p-value < 0.05; 3) fold change (mutant/WT) < 0.9. Up-regulated DEGs from KO adult hearts, satisfied the following criteria: 1) average FPKM in KO group > 2; 2) p-value < 0.05; 3) fold change (mutant/WT) > 1.1.
Gene Ontology (GO) enrichment analysis was performed using Novomagic
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each sample
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| Submission date |
Apr 23, 2024 |
| Last update date |
Jun 06, 2024 |
| Contact name |
Yang Li |
| E-mail(s) |
liyanganzhen@126.com
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| Phone |
86+13811892074
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| Organization name |
Beijing Anzhen Hospital
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| Street address |
Anzhen Road, Chaoyang District
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| City |
Beijing |
| ZIP/Postal code |
100029 |
| Country |
China |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE264733 |
Effect of depletion of C10orf71 on gene expression in hearts from embryonic mice at E18.5 and adult mice |
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| Relations |
| BioSample |
SAMN41064777 |
| SRA |
SRX24349886 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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