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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 06, 2018 |
| Title |
LFD BAT 1 |
| Sample type |
SRA |
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| Source name |
brown adipose tissue
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| Organism |
Mus musculus |
| Characteristics |
tissue: brown adipose tissue
strain: C57BL/6J
genotype: wild type
diet: standard rodent diet
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| Treatment protocol |
Diet
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction using E.Z.N.A® Total RNA kit II (Omega Bio-tek)
Libraries were sequenced as single-end 75 bp on Illumina NextSeq500 sequencing system at Cofactor Genomics Inc (St. Louis, MO). Approximately 30 millions of reads were retrieved from each sample
Ribosomal RNA was removed by using TruSeq Standard Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Remove Truseq3-SE adapter sequence using Trimmomatic (version 0.36)
Single-end sequencing reads were aligned to the mouse genome (ENSEMBL 84 release, GRCm38.p4) using RSEM (version 1.3.0)
Differential gene expression analysis was performed by DESeq2 (version 1.10.1) using the estimated gene-level counts from RSEM
RNA-Seq clean reads were mapped to mouse genome (ENSEMBL 84 release, GRCm38.p4)
Genome_build: GRCm38.p4
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| Submission date |
Apr 05, 2018 |
| Last update date |
Apr 06, 2018 |
| Contact name |
Haifei Shi |
| E-mail(s) |
shih@miamioh.edu
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| Phone |
5135293162
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| Organization name |
Miami University
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| Department |
Biology
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| Street address |
700 E High St
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| City |
Oxford |
| State/province |
Ohio |
| ZIP/Postal code |
45056 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE112740 |
RNA sequencing of brown adipose tissue of lean and obese mice |
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| Relations |
| BioSample |
SAMN08869073 |
| SRA |
SRX3889853 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3082783_SC22.RSEM.results.txt.gz |
2.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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