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Sample GSM2845676 Query DataSets for GSM2845676
Status Public on Nov 10, 2017
Title RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (0h_rep1)
Sample type SRA
 
Source name bone marrow
Organism Mus musculus
Characteristics genotype: wild type
treatment: cells differentiated in the presence of MCSF (0h)
age: 8-12 weeks
tissue: bone marrow-derived macrophages
Treatment protocol Cells were polarized on the 6th day of the differentiation with IL-4 (20ng/ml) for the indicated period of time.
Growth protocol Isolation and differentiation were completed as described earlier (Daniel et al., 2014). Isolated bone marrow-derived cells were differentiated for 6 days in the presence of L929 supernatant.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from cells using Tri Reagent (MRC) according to the manufacturer’s protocol.
Indexed cDNA libraries were prepared from 1 µg of total RNA following the TruSeq™ RNA Sample Preparation Kit (Illumina, Inc.) protocol. Briefly, the mRNA Poly-A was selected on oligo (dT) magnetic beads and fragmented by divalent cations at 94°C for 5 min. Reverse transcription was performed using SuperScript II reverse transcriptase (Life Technologies, Inc.) and random primers. After second strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. cDNA libraries were purified and size selected after PCR with AMPure XP beads (Beckman Coulter, Inc, Fullerton, C.A USA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description mm_BMDM_Wt_0h_ctrl_RNA_rep1
Data processing alignment with TopHat v2.0.7 using default parameters
calculating RPKM values by cufflinks v2.0.2 using default parameters
Genome_build: mm10
Supplementary_files_format_and_content: table (tsv) of expressed genes
 
Submission date Nov 08, 2017
Last update date May 15, 2019
Contact name Gergely Nagy
Organization name University of Debrecen
Department Department of Biochemistry and Molecular Biology
Street address Egyetem ter 1.
City Debrecen
ZIP/Postal code 4032
Country Hungary
 
Platform ID GPL17021
Series (2)
GSE106704 Characterization of transcriptional and epigenetic changes during mouse alternative macrophage polarization [RNA-Seq II]
GSE106706 Characterization of transcriptional and epigenetic changes during mouse alternative macrophage polarization
Relations
BioSample SAMN04868774
SRA SRX1924028

Supplementary file Size Download File type/resource
GSM2845676_mm_BMDM_Wt_0h_ctrl_RNA_rep1_fpkm_table.tsv.gz 488.5 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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