|
| Status |
Public on Jun 23, 2020 |
| Title |
Wild type, 6h, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow-derived dendritic cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Bone marrow-derived dendritic cells
strain: C57BL/6
genotype: Wild-type
treatment: Lipopolysaccharide 6 hours
|
| Treatment protocol |
BMDCs were left untreated (0 h) or stimulated with 10 ng/ml lipopolysaccharide (LPS) for 3, 6 or 9 h.
|
| Growth protocol |
Bone marrow-derived dendritic cells (BMDCs) were produced from bone marrow isolated from the femurs and tibias of 9-12 week old WT and TTP-/- mice.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using QIAzol Lysis Reagent, which was followed by chloroform extraction. RNA was precipitated using Isopropanol and GlycoBlue, and was consequently subject to DNA digestion using DNase.
Libraries were prepared using SENSE mRNA-Seq Library Prep Kit V2 (Lexogen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
6h.xlsx
|
| Data processing |
Cutadapt (https://doi.org/10.14806/ej.17.1.200) was used for barcode, adapter and quality trimming.
Quality control was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
STAR version 2.5 (Dobin et al. 2013) was used to map all remaining reads to the GRCm38/mm10 mouse genome assembly.
Differential expression analysis was performed based on read counts using DESeq2 (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: excel workbook files containing default DESeq2 result tables plus calculated individual FPKMs for each replicate
|
| |
|
| Submission date |
Jan 07, 2020 |
| Last update date |
Jun 23, 2020 |
| Contact name |
Pavel Kovarik |
| E-mail(s) |
pavel.kovarik@univie.ac.at
|
| Organization name |
University of Vienna
|
| Department |
Max Perutz Labs
|
| Street address |
Dr.-Bohr-Gasse 9/4
|
| City |
Wien |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE143241 |
Context-dependent IL-1 mRNA-destabilization by TTP prevents dysregulation of immune homeostasis |
|
| Relations |
| BioSample |
SAMN13746960 |
| SRA |
SRX7514225 |
