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Sample GSM4185021 Query DataSets for GSM4185021
Status Public on Dec 18, 2020
Title 56_GTAGAA: TPCA-1+TNFα replicate4
Sample type SRA
 
Source name bone marrow
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: Bone marrow-derived macrophages (BMDM)
treament: TPCA-1+TNFα
genotype: B6.129P2-Apoetm1Unc/J
Treatment protocol Cells were pretreated with either TMP195 (5 µM) or TPCA-1 (500 nM) for 1 h prior to stimulation with TNF-α (50 ng/ml) for 24 h.
Growth protocol Bone marrow-derived macrophages (BMDM) were generated as established by flushing the bone marrow from femurs and tibiae with ice-cold PBS, resuspending in PBS by repeated pipetting and filtering through a 40 µm cell strainer (BD Biosciences). After centrifugation of the cell suspension at 500 g for 10 min, the pellet was resuspended in culture medium (RPMI 1640 containing 10% FCS, 15% L929-cell-conditioned medium (LCM) and 100 µl/ml gentamycin) and plated on 15 cm untreated culture plates (Greiner). 15 % fresh LCM was added again on day 1 and 2 of culturing. For the stimulation experiments, differentiated macrophages were harvested by gentle scraping, transferred onto untreated 6-well or 12-well plates (Greiner) on Day 7 of culturing and left in LCM-free medium for 24 hours, allowing cells to adhere. Cells were then stimulated in FCS-free medium with either 50 ng/ml mouse recombinant TNF-α at different time intervals or left untreated.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Sequenced reads were mapped to mm10 whole genome using STAR 2.6.1d with default parameters
STAR 2.6.1d was used to obtain read counts per gene based on ENSEMBL annotation Mus_musculus.GRCm38.95.gtf.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include STAR gene-based read counts for each sample
 
Submission date Nov 21, 2019
Last update date Dec 18, 2020
Contact name Tobias Straub
E-mail(s) tstraub@med.uni-muenchen.de
Organization name LMU Munich
Department Biomedical Center, Bioinformatics
Street address Großhadener Str. 9
City Martinsried
ZIP/Postal code 82152
Country Germany
 
Platform ID GPL18480
Series (1)
GSE140783 Histone deacetylase 9 promotes vascular inflammation by activating IKK
Relations
BioSample SAMN13343753
SRA SRX7198256

Supplementary file Size Download File type/resource
GSM4185021_56.ReadsPerGene.out.tab.gz 268.5 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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