characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2020-04-18T17:04:26Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2019-10-07T13:29:37Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA6057139
characteristics.characteristic: External Id
characteristics.text: BAH-GU
characteristics.characteristic: INSDC center name
characteristics.text: 2020-04-18T17:04:26Z
characteristics.characteristic: INSDC first public
characteristics.text: 2019-10-07T13:29:37Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS3858271
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-8316:MK24
characteristics.characteristic: Submitter Id
characteristics.text: 60
characteristics.unit: year
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: monocyte
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000576
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: To obtain macrophages, CD14pos monocytes isolated from healthy donors (n=6) were plated in a 24-well plate in 3 ml complete medium (RPMI with 10% FCS, Penicillin/Streptomycin 100/U/ml and L-Glutamine 2mM) containing M-CSF (PeproTech) at the concentration of 50 ng/ml On day 3, macrophages were pre-treated with LPS (1 ng/ml) for 4h. For the last 2h, MerTK specific inhibitor, UNC106238 (Aobious) was added to a half of the wells at the concentration 250 uM. Cells were then washed with PBS and transwell inserts (0.4 um pore size) containing 3x105 Rheumatoid Arthritis FLS derived from 4 different patients (n=4) were added to the wells to generate a co-culture system. After 48h, FLS growing on the transwell inserts were moved into new 24 wells and lysed with RLT buffer with 1% beta-mercaptoethanol (Qiagen) and stored at -80oC till the RNA isolation step. We have 6 separate experiments with FLS from 4 different RA patients and macrophages from 6 different healthy donors. 2 FLS samples were used twice to react with distinct macrophage donors. FLS co-cultured with macrophages pre-treated with LPS and MerTK inhibitor are named FLS + Mac (LPS+MerTK inhibitor) RNA was isolated using RNEasy micro-kit (Qiagen). The samples containing FLS co-cultured with macrophages pre-stimulated with LPS are named FLS+Mac (LPS) while FLS co-cultured with macrophages pre-treated with LPS and MerTK inhibitor are named FLS + Mac (LPS+MerTK inhibitor). cDNA synthesis and amplification were performed by using SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (cat. no. 634890, Takara) starting with 10 ng of total RNA, following the manufacturers protocol. 10 ng of amplified cDNAs were sheared prior to preparing the final libraries using the Bioruptor® Pico system (Diagenode, 24 cycles of 30 sec on and 30 sec off)
characteristics.characteristic: description
characteristics.text: adult
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0001272
characteristics.characteristic: developmental stage
characteristics.text: rheumatic disease
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_1001161
characteristics.characteristic: disease
characteristics.text: SA104
characteristics.characteristic: individual
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: organism
characteristics.text: synovial membrane
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/FMA_66762
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000384
characteristics.characteristic: sex
characteristics.text: 1602
characteristics.characteristic: specimen
characteristics.text: MK24
characteristics.characteristic: title