|
| Status |
Public on Apr 23, 2015 |
| Title |
iWAT |
| Sample type |
SRA |
| |
|
| Source name |
inguinal adipose tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: B/C
age: 8-week-old
tissue: inguinal adipose tissue
|
| Treatment protocol |
RNAi in pre-adipocytes followed by induction of differentiation was performed as described (Sun et al., 2013)
|
| Growth protocol |
Primary fat tissues were isolated from 8-week-old B/C mice, and primary brown pre-adipocytes were isolated from 3~4-week-old mice and differentiated in culture as described (Sun et al., 2011)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using a Qiagen kit as described (Sun et al., 2011)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
low quality reads were removed using the fastq_quality_trimmer (“-t 20 -l 25” parameters) from the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Only reads in proper pairs were mapped to mm9 using TopHat v.2.0.4.12 (Trapnell et al., 2009) with default parameters and “--min-anchor 5”. The resulting junction files from the BAT, iWAT and eWAT samples were then concatenated and used for another run of TopHat using the --no-novel-juncs parameter.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Mar 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Juan R Alvarez-Dominguez |
| Organization name |
Harvard University
|
| Department |
Stem Cell and Regenerative Biology
|
| Street address |
7 Divinity Ave
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE66686 |
De novo Reconstruction of Adipose Tissue Transcriptomes Reveals Novel Long Non-coding RNAs that Regulate Brown Adipocyte Development |
|
| Relations |
| BioSample |
SAMN03394978 |
| SRA |
SRX913711 |
