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Sample GSM2538880 Query DataSets for GSM2538880
Status Public on Dec 19, 2017
Title Mo_GMCSF_IL4_0h_rep3
Sample type SRA
 
Source name Mo_GMCSF_IL4_0h
Organism Homo sapiens
Characteristics cell type: Mo-GMCSF[IL4 (0h)] cell
donor: 3
tissue: blood
Treatment protocol CD14+ monocytes were differentiated into (1) Mo-GMCSF[IL4 (0h)] cells by the addition of 800 IU/ml rhGM-CSF for 72 hours, (2) Mo-GMCSF[IL4 (0-72h)] or Mo-GMCSF[IL4 (0-144h)] cells by the addition of 800 IU/ml rhGM-CSF and 500 IU/ml rhIL4 for 72 or 144 hours, respectively, and (3) Mo-GMCSF[IL4 (12-144h)], Mo-GMCSF[IL4 (24-144h)], Mo-GMCSF[IL4 (48-144h)] or Mo-GMCSF[IL4 (72-144h)] cells by the addition of 800 IU/ml rhGM-CSF for the first 12, 24, 48 or 72 hours, respectively, and then 800 IU/ml rhGM-CSF and 500 IU/ml rhIL4 for the remaining hours until a final total duration of 144 hours
Growth protocol CD14+ monocytes were cultured in RPMI1640 medium supplemented with 10% FCS, 1% Penicillin-Streptomycin, 1% Sodiumpyruvate and 1% Glutamax (all from Gibco) for three days
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the miRNeasy Mini Isolation Kit (Qiagen), ribosomal RNA integrity was checked via a RNA assay on a Tapestation 2200 (Agilent)
TruSeq RNA Library Prep Kit v2 (Illumina) was used to generate libraries according to manufacturer‘s protocol. A DNA1000 assay for Tapestation 2200 (Agilent) was used to determine library fragment size and a qPCR quantification with a Library Quantification Kit for Illumina NGS libraries (Kapa Biosystems) on a Roche LightCycler480 was performed for quantification. Libraries were clustered to a TruSeq SR v3 flowcell and sequenced on a HiSeq1500 with 76bp+7ix reads
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Sequencing reads were retrieved as FASTQ files and then demultiplexed using CASAVA software suite version 1.8.2
Reads were aligned against the human genome version hg19 using TopHat version v2.1.0 (Kim et al., 2013); all default options were used
BAM files were sorted according to the mapping position and then imported into Partek® Genomics Suite® software, version 6.6 Copyright©; 2017 (PGS)
Quantification of mRNA was performed against the hg19 RefSeq Transcripts database version 2015-08-04 to obtain read counts for each individual RefSeq gene; 20,359 genes were finally retrieved
The obtained read count table was normalized using the R package DESeq2 (Love et al., 2014) and were then imported back into PGS
Normalized read counts were batch corrected to remove the unwanted variation introduced by donor
Then, genes were reduced to those with a mean normalized read count of 10 in at least one of the investigated groups, leading to 12,794 genes
All normalized count values smaller than 1 were set to 1 to avoid spurious Fold-Changes later on
Genome_build: hg19
Supplementary_files_format_and_content: TAB-delimited text file containing normalized abundance measurements for a filtered list of genes (see processing steps)
 
Submission date Mar 16, 2017
Last update date May 15, 2019
Contact name Joachim Schultze
E-mail(s) j.schultze@uni-bonn.de
Organization name LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)
Department Genomics and Immunoregulation
Street address Carl-Troll-Strasse 31
City Bonn
State/province NRW
ZIP/Postal code 53115
Country Germany
 
Platform ID GPL18460
Series (2)
GSE96715 Time-dependent regulation of cellular programming of monocytes by NCOR2 [RNASeq_TK]
GSE96719 Time-dependent regulation of cellular programming of monocytes by NCOR2
Relations
BioSample SAMN06608471
SRA SRX2647142

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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