|
| Status |
Public on Nov 08, 2024 |
| Title |
human white adipocyte cell line, Control, m6A IP, biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
white adipocyte cell
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: WT
cell type: white adipocyte cell
|
| Growth protocol |
All mice were fed with chow-diet for twenty-four weeks from four week of age. At the end of the experiment, mice were euthanized after overnight fasting, followed by serum and tissue sample collection.
Cells were differentiated for 21 days, washed with PBS and cultured in 1% BSA containing high-glucose DMEM medium for 24 hours, and then collected cell pallet for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was then extracted from iBAT/iWAT by TRIzol. 1 μg of mRNAs was isolated from total RNA using a Dynabeads mRNA DIRECT purification kit (Thermo Fisher). Then, mRNA was adjusted to about 10 ng μl−1 in 100 μl and fragmented using a Bioruptor ultrasonicator (Diagenode) with 30 s on/off for 30 cycles. m6A immunoprecipitation (m6A-IP) and library preparation were performed using the EpiMark N6-Methyladenosine enrichment kit (NEB).
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
hWAT.RADAR.csv
hWAT.siKD.RADAR.csv
hWAT_hBAT.RADAR.csv
CF02IP
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (4.2)
Trimmed sequence reads were mapped to mm10 using HISAT2 (2.2.1).
Read count extraction and differential expression levels of exons and genes were analyzed using RADAR (0.2.4) followed by DEseq2 (1.36.0).
For differential m6A regions of mRNA, RADAR software (0.2.4) was used as well.
Assembly: mm10 (GRCm38.102), hg38 (GRCh38.107)
Supplementary files format and content: DESeq2 results with normalized reads for each sample and m6A analysis results from RADAR
|
| |
|
| Submission date |
Dec 13, 2023 |
| Last update date |
Nov 08, 2024 |
| Contact name |
Cheng-Wei Ju |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Chicago
|
| Lab |
Chuan He Lab
|
| Street address |
929 East 57th Street, GCIS, Room E313
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE250137 |
METTL14-mediated m6A differentially orchestrates brown and white adipose tissue transcriptomes to regulate systemic metabolism |
|
| Relations |
| BioSample |
SAMN38814408 |
| SRA |
SRX22881553 |
