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| Status |
Public on Jan 30, 2020 |
| Title |
Rosi_rep2_68 |
| Sample type |
SRA |
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| Source name |
brown adipose tissue
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| Organism |
Mus musculus |
| Characteristics |
tag: F1
tissue: brown adipose tissue
age: 8 weeks
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| Treatment protocol |
Male F1 intercross progeny of C57BL/6J and 129S1SvImJ mice (Jackson Labs stock number: JAX 101043) mice received for two weeks a control low fat diet (Research Diets D12450B, n=5), or the same diet wtih 0.005% rosiglitazone (n=5), or with 0.2% fenofibrate (n=5).
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| Growth protocol |
Mice were housed at room tempature and received normal chow diet for the first 8 weeks of life.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Brown adipose tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Paired-end sequencing libraries using the NEBNext Ultra RNA library preparation kit according to the manufacturer’s instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
LFD + Rosi
Rosi_rep2_68
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| Data processing |
Raw sequenced reads were filtered to retain only high-quality reads. In addition, ribosomal reads and repeats were eliminated by NGSC. Remaining reads were processed with RNA-Seq Unified Mapper (RUM)
RUM aligns reads to the set of known transcripts included in RefSeq, UCSC known genes, and ENSEMBL transcripts, and the genome, and outputs feature-level quantitation (transcript, exon, and intron).
To analyze global gene expression profiles, the number of uniquely aligning read counts to mRNA transcripts in RefSeq were extracted from the RUM output and processed using a custom script to carry out differential expression analysis using Bioconductor software’s package edgeR to compute a p-value and fold-change for each transcript.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
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| Submission date |
Jan 29, 2020 |
| Last update date |
Feb 01, 2020 |
| Contact name |
Yachen Shen |
| E-mail(s) |
[email protected]
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| Phone |
2677215430
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| Organization name |
University of Pennsylvania
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| Street address |
3400 Civic Center Blvd, Philadelphia, PA 19104
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| City |
Philadelphia |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE144490 |
Shared PPARα/γ target genes regulate brown adipocyte thermogenic function (RNA-Seq) |
| GSE144491 |
Shared PPARα/γ target genes regulate brown adipocyte thermogenic function |
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| Relations |
| BioSample |
SAMN13941144 |
| SRA |
SRX7647789 |
| 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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