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Sample GSM1177233 Query DataSets for GSM1177233
Status Public on Jan 03, 2014
Title Macrophages wild type +LPS
Sample type SRA
 
Source name Macrophages wild type +LPS
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: bone marrow derived macrophages
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 SAMN02216894
SRA SRX316621

Supplementary file Size Download File type/resource
GSM1177233_AE12_R1.TXT.gz 3.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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