organism: Homo sapiens
description: Protocols: The THP-1 monocytic cell line obtained from ATCC (#TIB-202) was used. Approximately 1 million cells were used for each biological replicate. 3 biological replicates were cultured and stimulated independently. THP-1 cells were cultured in RPMI 1640 medium (Biochrom, #FG1215) supplemented with 10% fetal bovine serum (FBS, Biochrom, #S0615).THP-1 cells were seeded from frozen ATCC stocks (5x106cells/ml), incubated at 37°C in a 5% CO2 atmosphere. Sub culturing was done by adding fresh medium to reach a cell concentration of 2x105 cells/ml. Medium was completely renewed every week. All treatment compounds were added to the standard growth medium. THP-1 monocytes were differentiated to macrophages with 10 nM phorbol-12-myristate-13-acetate (PMA, Sigma, #P8139-5MG) for 48 hours. Following differentiation, cell were stimulated with 0.06 mM BSA (BSA, Sigma-Aldrich, #A7030) and 0.4mM NaOH (Sigma Aldrich, #72068) for 24 hours in the presence of 10 nM PMA or left unstimulated. Unstimulated macrophages were incubated in renewed growth medium with 10nM PMA. RNA extraction was performed using RNeasy Mini Kit from Qiagen (#74106) using the standard procedure with 30 min on-column DNase digestion. RNA concentration and quality was controlled using NanoDrop 2000 (Thermo Fisher Scientific) and Bioanalyser 2100 (Agilent). Sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, #RS-122-2001) according to the standard procedure.
attributes.tag: ENA first public
attributes.value: 2018-02-10
attributes.tag: ENA last update
attributes.value: 2018-01-31
attributes.tag: External Id
attributes.value: SAMEA104556796
attributes.tag: INSDC center alias
attributes.value: Laboratory for Functional Genomics, Nutrigenomics and Systems Biology, Scientific Genomics Platforms, Max Delbruck Center for Molecular Medicine (BIMSB/BIH)
attributes.tag: INSDC center name
attributes.value: Laboratory for Functional Genomics, Nutrigenomics and Systems Biology, Scientific Genomics Platforms, Max Delbruck Center for Molecular Medicine (BIMSB/BIH)
attributes.tag: INSDC first public
attributes.value: 2018-02-10T17:01:52Z
attributes.tag: INSDC last update
attributes.value: 2018-01-31T10:02:24Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-6439:BSA_2
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell line
attributes.value: THP-1
attributes.tag: cell type
attributes.value: macrophage
attributes.tag: common name
attributes.value: human
attributes.tag: disease
attributes.value: acute monocytic leukemia
attributes.tag: organism part
attributes.value: blood
attributes.tag: progenitor cell type
attributes.value: monocyte
attributes.tag: sample name
attributes.value: E-MTAB-6439:BSA_2
attributes.tag: stimulus
attributes.value: phorbol 13-acetate 12-myristate (10 nanomolar)