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| Status |
Public on Oct 02, 2022 |
| Title |
liver HS-3 [LHS3] |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
strain: ICR
tissue: liver
age: 10 weeks
treatment: High fat diet & STZ
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| Extracted molecule |
total RNA |
| Extraction protocol |
Liver were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used tp abtain 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 |
MGISEQ-2000RS |
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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 mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m
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: mm10
Supplementary_files_format_and_content: gene expression
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| Submission date |
Jun 29, 2021 |
| Last update date |
Oct 02, 2022 |
| Contact name |
Yong Zhao |
| E-mail(s) |
yzhao818@hotmail.com
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| Phone |
86-18661613617
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| Organization name |
Qingdao Agricultural University
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| Department |
College of Life Sciences
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| Lab |
B604
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| Street address |
700 Changcheng Road
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| City |
Qingdao |
| State/province |
Shandong |
| ZIP/Postal code |
266109 |
| Country |
China |
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| Platform ID |
GPL30215 |
| Series (1) |
| GSE179098 |
AOS10-FMT could rescure the adverse effects of high fat diet & STZ on the liver [liver_RNA-seq] |
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| Relations |
| BioSample |
SAMN19930737 |
| SRA |
SRX11248190 |
| 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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