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Sample GSM1625969 Query DataSets for GSM1625969
Status Public on Feb 28, 2016
Title M-baseline-3
Sample type SRA
 
Source name unstimulated primary human macrophages
Organism Homo sapiens
Characteristics donor: 3
cell type: human monocyte derived macrophages
stimulated with: none (unstimulated)
Treatment protocol Fractions of baseline macrophages were further stimulated for 72h in culture medium with the addition of a combination of TNF-α (800U/ml), PGE2 (1µg/ml) and Pam3CSK4 (1µg/ml) (=TPP) to differentiate macrophages into subtypes
Growth protocol MACS beads isolated CD14 primary human monocytes were cultured for 72 h with granulocyte/macrophage colony stimulating factor (GM-CSF; 500U/ml) in RPMI1640 medium containing 10 % fetal calf serum (FCS) and 1% Penicillin/Streptomycin to generate unstimulated baseline macrophages
Extracted molecule polyA RNA
Extraction protocol Cultured macrophages were lysed in TRIZOL (Invitrogen) and total RNA was extracted according to the manufacturers’ protocol
1µg of total RNA was converted to RNA-seq libraries according to manufacturers' protocol with Illumina TruSeq RNA Sample Preparation Kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiScanSQ
 
Description Mb-1
Normalized-RNA-seq-tag-counts-annotated.txt
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with TopHat2 (v2.0.3) against the hg19 reference genome (RefSeq database release 64).
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.0.2) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10. Sequencing datasets for M-IFNy and M-IL4 are available on Gene expression omnibus (GEO) platform with reference number GSE36952 labeled as M1 and M2 macrophages.
Genome_build: hg 19
Supplementary_files_format_and_content: Normalized RNA-seq tag counts annotated to the hg19 reference genome for three independent biological replicates
 
Submission date Mar 05, 2015
Last update date May 15, 2019
Contact name Joachim Schultze
E-mail(s) [email protected]
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 GPL15456
Series (2)
GSE66593 Epigenomic landscapes of human inflammation associated macrophages [RNA-seq]
GSE66595 Epigenomic landscapes of human inflammation associated macrophages
Relations
BioSample SAMN03389879
SRA SRX903241

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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