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Sample GSM3565012 Query DataSets for GSM3565012
Status Public on May 15, 2020
Title PolyA_PEC_wt_UT_R2
Sample type SRA
 
Source name Peritoneal Exudate Macrophages (PEC)
Organism Mus musculus
Characteristics strain: C56Bl6/J
genotype: wild type
cell type: Peritoneal Exudate Macrophages (PEC)
treatment: Untreated
Treatment protocol 5 million PECs were plated in RPMI1640 containing 10% FBS and left untreated or stimulated with 200U/ml interferon gamma for 4 hours.
Growth protocol PEC were harvested from mice injected with 500 L of 3% (wt/vol) thioglycollate medium (Difco) 4 days before isolation
Extracted molecule polyA RNA
Extraction protocol The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented into small fragments using divalent cations and elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. cDNA fragments were end-repaired and a single ‘A’ base was added before adapter ligation. The products were then purified and enriched by PCR to create the final cDNA library.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description Standard_CPM_PECs.xls
Data processing Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches and with a mean distance between pairs (-r) of 250bp
Transcripts abundance were quantified using HTSeq (PMID: 25260700)
Differentially expressed genes were called using edgeR (PMID: 19910308)
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus UCSC iGenome
Supplementary_files_format_and_content: Counts per million (CPM) mapped reads obtained using edgeR
 
Submission date Jan 16, 2019
Last update date May 15, 2020
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 GPL9250
Series (1)
GSE84468 Tumor-derived prostaglandin E2 promotes p50 NF-κB-dependent differentiation of monocytic MDSC.
Relations
BioSample SAMN10756492
SRA SRX5255288

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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