|
| Status |
Public on Aug 28, 2020 |
| Title |
RNA sequencing of iBAT 4 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse whole adipose tissue depot
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: iBAT
|
| Treatment protocol |
No treatment applied to adipose tissue depots
|
| Growth protocol |
For miRNAseq, total RNA was extracted from fat pads of 13-week old C57BL/6J male mice housed at room temperature and from inguinal fat pads of 13-week old mice housed at 4° C for 1 week prior to sacrifice. For mRNAseq, iBAT and eWAT tissue was dissected from 15-week old C57BL/6J male mice and immediately flash frozen in liquid nitrogen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from tissues and cells using a TRIzol (Invitrogen)/chloroform extraction, followed by purification with RNeasy mini kits (Qiagen). To retain small RNAs during RNA purification, 1.5X volumes of 100% ethanol was used to precipitate RNA prior to column loading and RW1 buffer was substituted with RWT (Qiagen).
For miRNA, The TruSeq Small RNA Library Prep Kit (Illumina) was used to prepare libraries for sequencing, which was performed by LC Sciences. For mRNA, the library was prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit, and sequencing was performed on an Illumina NextSeq 500 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw counts per transcript were determined by pseudo alignment tool Kallisto (version: 0.45.0) to mouse index GRCm38 (version: 10)
Per gene abundance measurements were calculated for each sample in R (version: 3.6.1) using package TxImport (version: 1.14.2)
Normalized abundance and log2FoldChange measurements were calculated using DESeq2 output, method "apelgm" (version: 1.26.0)
Genome_build: mm10
Supplementary_files_format_and_content: DEseq normalized counts of miRNA seq.csv
Supplementary_files_format_and_content: DEseq normalized counts of mRNA seq.csv
|
| |
|
| Submission date |
Aug 28, 2020 |
| Last update date |
Aug 29, 2020 |
| Contact name |
Sean O'Connor |
| E-mail(s) |
soconnor@rockefeller.edu
|
| Organization name |
Rockefeller University
|
| Department |
Laboratory of Molecular Metabolism
|
| Lab |
Paul Cohen
|
| Street address |
1230 York Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE142677 |
AGO HITS-CLIP Reveals Distinct Patterns of miRNA Regulation of Visceral and Brown Adipose Tissue Identity |
|
| Relations |
| BioSample |
SAMN15931874 |
| SRA |
SRX9029656 |
