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| Status |
Public on Dec 05, 2023 |
| Title |
Muscle tissue, KO1 |
| Sample type |
SRA |
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| Source name |
tissue
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| Organism |
Mus musculus |
| Characteristics |
cell line: tissue
cell type: tissue
genotype: mKD
treatment: mKD
time: 48h
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Fibrous Tissue Mini Kit (74704, Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Jan 30, 2023 |
| Last update date |
Dec 05, 2023 |
| Contact name |
Haining Lyu |
| E-mail(s) |
haining.lyu@yale.edu
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| Phone |
2036278343
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| Organization name |
Yale
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| Street address |
1145 chapel street, 401
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| City |
New Haven |
| State/province |
Connecticut |
| ZIP/Postal code |
06511 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE224042 |
Effect of TET3 expression on muscle insulin sensitivity |
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| Supplementary data files not provided |
| Raw data not provided for this record |
| Processed data are available on Series record |
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