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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 15, 2021 |
| Title |
heart, saline-injected control mice_4 |
| Sample type |
SRA |
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| Source name |
heart
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Heart
age: 8 weeks old
stress: saline
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| Extracted molecule |
total RNA |
| Extraction protocol |
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample, FPKMs
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| Submission date |
Oct 12, 2021 |
| Last update date |
Oct 15, 2021 |
| Contact name |
Xiaoping Wang |
| E-mail(s) |
XiaopingWang726@outlook.com
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| Phone |
+8617702206558
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| Organization name |
Beijing University of Chinese Medicine
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| Street address |
No. 11, North 3rd Ring East Road, Chaoyang District, Beijing
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100029 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE185754 |
Cardiomyocyte TLR4 regulates autophagy through TRAF6-mediated TFEB ubiquitination in sepsis-associated cardiac dysfunction |
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| Relations |
| BioSample |
SAMN22228512 |
| SRA |
SRX12580380 |
| 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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