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| Status |
Public on Mar 01, 2022 |
| Title |
TH-treated NASH |
| Sample type |
SRA |
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| Source name |
TH
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
diet: western diet with liquid fructose
treatment: treated with thyroid hormone for 8 weeks
tissue: liver
gender: male
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| Treatment protocol |
Tenweek old male C57BL/6J normal chow diet (NCD) or WDF for 16 weeks, at which point half of the WDF-fed mice began receiving T3 (35 ng/g mice) and T4 (7 ng/g mice) in 15% (w/v) fructose drinking water for the next 8 weeks
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The liver tissue was homogenized in Qiazol, followed by extraction using
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using a specialized kit that leaves the mRNA. The mRNA from either eukaryotic or prokaryotic sources is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.
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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 |
data assesment
mapping to referenced genome using TopHat2
FPKM value was used to determine the expression level, which was generated using HTSeq software
differential expression analysis with Log2 (fold change>1) and q-value<0.005
Go enrichemnt analysis
Supplementary_files_format_and_content: FPKM value for each sample
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| Submission date |
Apr 19, 2021 |
| Last update date |
Mar 01, 2022 |
| Contact name |
Jin Zhou |
| E-mail(s) |
[email protected]
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| Organization name |
Duke-NUS Medical School
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| Department |
CVMD
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| Street address |
8 College Road
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| City |
Singapore |
| ZIP/Postal code |
169857 |
| Country |
Singapore |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE172297 |
RNA-seq analysis of control, NASH, and TH-treated NASH liver |
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| Relations |
| BioSample |
SAMN18794841 |
| SRA |
SRX10632322 |
| 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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