|
| Status |
Public on Dec 11, 2023 |
| Title |
RNAseq_SV_HFD_3 [F_SV_109_5] |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129S1/SvImJ
diet: HFD
mouse id: F_SV_109_5
tissue: Liver
replicate: 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from mouse liver tissue was extracted using the miRNeasy Mini Kit (QIAGEN) and QIAzol Lysis Reagent (QIAGEN) according to the manufacturer's protocol. Extracted RNA was treated with DNase using RNase-Free DNase (QIAGEN).
Ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit (New England BioLabs). Libraries were prepared using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs) following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw reads were trimmed with Trimmomatic (v0.36) using long TruSeq3-SE.v2 adapters and as essential settings: ILLUMINACLIP:0:30:10, LEADING:3, TRAILING:3, MINLEN:35.
Bowtie (v.2.2.3) was used to identify reads that align to known possible contaminants, which were then discarded.
Reads were then aligned to strain specific genomes, generated with g2gtools (v0.2.9) and MGPv5 SNPs and InDels, using STAR (v2.5.4b). Alignment was done using manual two-pass alignment: After first alignment the splice junctions were collected and used on the second pass alignment with ‘–sjdbFileChrStartEnd’ parameter along with the 2nd pass index generated with the splice junctions. STAR parameters were as follows: --outFilterMultimapNmax 100 –outFilterMismatchNmax 33 –seedSearchStartLmax 12 –alignSJoverhangMin 15 –outFilterMatchNminOverLread 0 –outFilterScoreMinOverLread 0.3 –outFilterType BySJout).
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts: Read counts for genes were generated using STARs ‘-quantMode GeneCounts’ option. Gene IDs are ENSEMBL IDs from Gencode M17 annotation.
Supplementary_files_format_and_content: VST normalized counts: Normalized counts were generated using DESeq2 (v1.26.0) for blind VST normalization.
|
| |
|
| Submission date |
Feb 17, 2022 |
| Last update date |
Dec 11, 2023 |
| Contact name |
Juho Mikael Mononen |
| E-mail(s) |
juho.mononen@uef.fi
|
| Organization name |
University of Eastern Finland
|
| Department |
Faculty of Health Sciences
|
| Lab |
Heikkinen lab
|
| Street address |
Yliopistonranta 1E
|
| City |
Kuopio |
| ZIP/Postal code |
70210 |
| Country |
Finland |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE196941 |
Genetic determinants of TCF7L2 binding and chromatin availability in mouse liver [RNA-seq] |
| GSE196942 |
Genetic determinants of TCF7L2 binding and chromatin availability in mouse liver |
|
| Relations |
| BioSample |
SAMN26020245 |
| SRA |
SRX14209222 |
