|
| Status |
Public on Aug 05, 2023 |
| Title |
hypothalamus, WD, Tas1r3-/-, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
hypothalamus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: hypothalamus
genotype: Tas1r3-/-
treatment: western diet (WD)
time: 12 week
Sex: Male
|
| Treatment protocol |
Western diet (60% fat diet, D12492 and 30% sucrose solution) and normal diet (10% fat diet, D12540J with plain water) were provided for 12 weeks.
|
| Growth protocol |
Tas1r3-/- mice weighing 23–25 g and age- and weight -matched WT littermates were housed in a specific pathogen-free (SPF) animal facility.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were euthanized by intraperitoneal injection of 20% urethane and the hypothalamus of mice was isolated and snap frozen in liquid nitrogen. RNA was isolated using RNAqueous (AM1914, Ambion) according to the manufacturer’s protocol.
Dynabeads mRNA DIRECT Micro Kit (Ambion) was used to isolate Intact mRNA. The total mRNA samples were depleted of up to 99.9% of 5S, 5.8S, 18S, and 28S rRNA using the RiboMinus Eukaryote System v2 (Life Technologies, Carlsbad, CA, USA). Barcoded cDNA libraries were constructed from the rRNA-depleted mRNA samples and prepared using the Ion Total-RNA Seq Kit v2 (Life Technologies).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Sequenced reads were mapped to mm39 whole genome and Refseq transcripts 93 using STAR method.
After mapping and aligning, the resulting BAM files were imported into Partek® Genomics Suite software v6.3 (Partek Inc.) (http://www.partek.com/partekgs) and converted into gene transcript levels as fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: mm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Oct 19, 2022 |
| Last update date |
Aug 05, 2023 |
| Contact name |
Jaewon Song |
| E-mail(s) |
sjw9509@gmail.com
|
| Organization name |
Seoul National University
|
| Street address |
Gwanak-gu
|
| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE216063 |
Deficiency of hypothalamic taste receptor type 1 member 3 prevents western diet-induced anxiety in mice |
|
| Relations |
| BioSample |
SAMN31362126 |
| SRA |
SRX17952595 |
