|
| Status |
Public on Jul 22, 2024 |
| Title |
2.5_BAT_A_FPKM |
| Sample type |
SRA |
| |
|
| Source name |
brown adipose tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brown adipose tissue
strain: C57Bl6J
Sex: male
genotype: WT
age: 10 weeks
|
| Treatment protocol |
Male C57Bl6J mice were housed under controlled conditions at 22 ±2 °C in an 12/12-hour light/dark cycle maintained on a standard chow diet (Ssniff, Soest, Germany). The animals were killed at 10 weeks of age by cervical dislocation. Brown adipose tissue depots were isolated and immediately frozen in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from 50 mg of tissue that was homogenized by grinding frozen tissue on liquid nitrogen. A 50 mg aliquot of tissue powder was then removed for RNA isolation.
NGS sequencing was conducted using Illumina HiSeq 2000 with 2 x 100 bp reads (LGC genomics, Berlin, Germany).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
sample_2
|
| Data processing |
Read pre-processing: Demultiplexing of all libraries for each sequencing lane using the Illumina bcl2fastq 1.8.4 software: 1 or 2 mismatches or Ns were allowed in the barcode read when the barcode distances between all libraries on the lane allowed for it. Clipping of Illumina TruSeq™ adapters of all reads (folder 'AdapterClipped'): reads with final length < 20 bases were discarded. Filtering of rRNA sequences using RiboPicker 0.4.3 (http://ribopicker.sourceforge.net/) (folder 'RiboPicker') Creation of FastQC reports for all FASTQ files
For data processing and analysis, FASTQC v0.11.8 was used for quality assessment and trimmgalore v0.6.4 was applied for filtering adapter sequences and small reads.
The clean reads were mapped to a reference genome (Genome Reference Consortium Mouse Build 38 mm10) using the alignment tools HISAT2 v2.1.0 and Bowtie2 v2.3.5.1 Expression levels were quantified Cufflinks v.2.2.1.
Assembly: Genome Reference Consortium Mouse Build 38 mm10
Supplementary files format and content: normalized_FPKM_gene_expression
|
| |
|
| Submission date |
Jun 04, 2024 |
| Last update date |
Jul 22, 2024 |
| Contact name |
Tim Julius Schulz |
| Organization name |
German Institute of Human Nutrition
|
| Street address |
Arthur-Scheunert-Allee 114-116
|
| City |
Nuthetal |
| ZIP/Postal code |
14558 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE269003 |
Analysis of gene expression patterns in brown adipose tissue |
|
| Relations |
| BioSample |
SAMN41669878 |
| SRA |
SRX24792828 |
