|
| Status |
Public on Feb 01, 2024 |
| Title |
iscWAT_old_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
interscapular adipose tissue
|
| Organism |
Monodelphis domestica |
| Characteristics |
tissue: interscapular adipose tissue
age: 10 weeks
gender: f
animal id: 1731
developmental stage: old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from three different adipose tissue depots (anterior subcutanous, inguinal, interscapular) using Qiazol according to the manufacturer’s instructions (Qiazol Lysis Reagent, Qiagen).
Paired-end: After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. After a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment. Single-end: Libraries were prepared by isolating total RNA from fat tissue homogenized in TRIzol reagent. Total RNA was converted to cDNA and then to sequencing-ready barcoded Illumina libraries with the NUGEN complete RNAseq kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Sequencing reads were aligned with STAR Mapper v2.7.8a using Ensembl gene annotations.
Count files were created using STAR counts.
Assembly: Monodelphis domestica reference genome (ASM229v1) using Ensembl gene annotations.
Supplementary files format and content: csv countfiles, raw reads, Ensembl Gene Annotation
|
| |
|
| Submission date |
Feb 02, 2023 |
| Last update date |
Feb 01, 2024 |
| Contact name |
Dominik Lutter |
| E-mail(s) |
dominik.lutter@helmholtz-muenchen.de
|
| Organization name |
Helmholtz Zentrum München
|
| Department |
Institute for Diabetes and Obesity
|
| Street address |
Ingolstädter Landstraße 1
|
| City |
Neuherberg |
| ZIP/Postal code |
D-85764 |
| Country |
Germany |
| |
|
| Platform ID |
GPL27874 |
| Series (1) |
| GSE224318 |
Gene expression signature of three different fat depots of Monodelphis domestica of different ages |
|
| Relations |
| BioSample |
SAMN33016864 |
| SRA |
SRX19257541 |
