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| Status |
Public on Aug 15, 2022 |
| Title |
LSW_123 |
| Sample type |
SRA |
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| Source name |
Liver cells
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: liver
age: 17 weeks
sample_common_id_with adipose_tissue: 62415_3
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| Extracted molecule |
total RNA |
| Extraction protocol |
Liver tissue were dissected, and then snap-frozen. RNA was extracted using Trizol
Library preps were created using Illumina kits and run on an Illumina HiSeq 2500 to obtain 37bp paired-end reads for liver
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
LSW_123
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| Data processing |
alignment reads to the reference to generate the BAM files, using STAR
sort the raw bam files and mark duplications using Picard
assemble the GTF reference file based on your BAM files using CUFFLINK and CUFFMERGE
estimate the gene counts and then calculate the RPKMs using featureCounts and DESeq2
normalize the RPKMs of each gene and detect the significant different expression genes [using DESeq2]
Assembly: Rn6.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Apr 07, 2022 |
| Last update date |
Aug 15, 2022 |
| Contact name |
Thu Hong Le |
| E-mail(s) |
[email protected]
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| Organization name |
UCL
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| Street address |
Gower Street
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| City |
London |
| ZIP/Postal code |
WC1E 6BT |
| Country |
United Kingdom |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE200453 |
Genetic mapping of multiple metabolic traits identifies novel genes for adiposity, lipids and insulin secretory capacity in outbred rats II |
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| Relations |
| BioSample |
SAMN27407074 |
| SRA |
SRX14781289 |
| 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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