|
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 |