|
| Status |
Public on Jan 03, 2014 |
| Title |
Dendritic cells wild type +eLDL |
| Sample type |
SRA |
| |
|
| Source name |
Dendritic cells wild type +eLDL
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: bone marrow derived dendritic cells
|
| Treatment protocol |
At day 8-9 of culture, DCs were matured by overnight stimulation with either 200 ng/ml LPS (Sigma-Aldrich), 5 µg/ml Pam3Cys (EMC Microcollections), 5 ng/ml TNFα (PeproTech), or 100 µg/ml Curdlan (Sigma-Aldrich), respectively.
|
| Growth protocol |
Wildtype (C57BL/6) and mir-155-/- (To-Ha Thai et al., Science, 2007, B6.Cg-Mir155tm1.1Rsky/J, JAX) mice used in this study were bred and maintained in a conventional animal facility according to local regulations, and sacrificed at 8 to 12 weeks of age for use in experiments. DCs were generated as described previously (Lutz et al., J Immunol Methods, 1999). In brief, flushed bone marrow from femur and tibia was cultured in R10 culture medium (RPMI 1640 supplemented with 10 % fetal calf serum, L-Glutamine and Penicillin/Streptomycin, all from Life Sciences) supplemented with GM-CSF hybridoma supernatant.Macrophages were differentiated according to the DC culture but using M-CSF hybridoma supernatant instead of GM-CSF (Rutherford et al., J. Leukoc. 1992).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested, lysed in Trizol and total RNA was extracted according to the manufacturere's protocol.
Libraries were constructed according to Illumina's TruSeq cloning kit using the following adapters: 5′adapter 5′-GUUCAGAGUUCUACAGUCCGACGAUC-3′; 3′adapter Phospho-TGGAATTCTCGGGTGCCAAGG-Amino-C7. Barcoding was performed on the PCR level.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
small RNA sequencing data
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Adapter trimming was performed using custom scripts. Aggregation of identical sequences resulted in processed TXT-files
Reads were mapped to miRBase 19, Mus musculus using custom scripts
Supplementary_files_format_and_content: tab-delimited TXT-file; trimmed read sequence followed by a tab and the number of reads
|
| |
|
| Submission date |
Jun 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Anne Dueck |
| E-mail(s) |
anne.dueck@tum.de
|
| Organization name |
TUM
|
| Department |
Institute of Pharmacology and Toxicology
|
| Street address |
Biedersteiner Str.29
|
| City |
Munich |
| State/province |
Bavaria |
| ZIP/Postal code |
80802 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15103 |
| Series (1) |
| GSE48404 |
A miR-155-ruled microRNA hierarchy in dendritic cell maturation and macrophage activation |
|
| Relations |
| BioSample |
SAMN02216905 |
| SRA |
SRX316613 |
