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Sample GSM2241174 Query DataSets for GSM2241174
Status Public on Mar 02, 2017
Title poly(A) mRNA IL4_2h_R2
Sample type SRA
 
Source name Primary bone marrow-derived macrophages (BMDM)
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: BMDM cells (7th day of differentiation)
Treatment protocol Macrophages were subjected to different treatment (see individual samples for details)
Growth protocol Bone marrow cells isolated from C57BL/6 mice were plated in 10 cm plates in 10ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol).
Extracted molecule polyA RNA
Extraction protocol Used TruSeq RNA kit (Illumina) starting from polyA mRNA
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description treatment: IL4 (10 ng/ml) for 2hrs
Processed data file: CPM.TABLE.READS.txt
Data processing Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm10 genome and transcripts using TopHat v2.1.0 (PMID: 23618408), allowing up to two mismatches and the option --b2-very-sensitive
Transcripts abundance were quantified using HTSeq (PMID: 25260700)
Differentially expressed genes were called using edgeR (PMID: 19910308)
Genome_build: mm10 (Genome Reference Consortium GRCm38), transcripts from Mus Musculus UCSC iGenome
Supplementary_files_format_and_content: Counts per million (CPM) mapped reads obtained with edgeR
 
Submission date Jul 18, 2016
Last update date May 15, 2019
Contact name Viviana Piccolo
E-mail(s) viviana.piccolo@ieo.it
Organization name European Institute of Oncology (IEO)
Department Department of Experimental Oncology
Lab Gioacchino Natoli Lab
Street address Via Adamello 16
City Milano
State/province Milano
ZIP/Postal code 20139
Country Italy
 
Platform ID GPL13112
Series (2)
GSE84517 Opposing macrophage-polarization programs show extensive epigenomic and transcriptional cross-talk [RNA-Seq]
GSE84520 Opposing macrophage-polarization programs show extensive epigenomic and transcriptional cross-talk
Relations
BioSample SAMN05414037
SRA SRX1958793

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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