characteristics: ERC000011
characteristics: ENA-CHECKLIST
characteristics: 2022-10-20T00:17:32Z
characteristics: ENA-FIRST-PUBLIC
characteristics: 2022-10-20T00:17:32Z
characteristics: ENA-LAST-UPDATE
characteristics: SAMEA110188690
characteristics: External Id
characteristics: BioMed X GmbH
characteristics: INSDC center name
characteristics: 2022-10-20T00:17:32Z
characteristics: INSDC first public
characteristics: 2022-10-20T00:17:32Z
characteristics: INSDC last update
characteristics: public
characteristics: INSDC status
characteristics: ERS12287493
characteristics: SRA accession
characteristics: E-MTAB-11791:Syn_Bio_078
characteristics: Submitter Id
characteristics: ArrayExpress
characteristics: broker name
characteristics: human
characteristics: common name
characteristics: Protocols: For protocol 2, as described by Edalat G. S. et al. (steps in bold differ between the two protocols): 1. Fresh tissue fragments, obtained by synovial biopsy were placed on 70 μm cell strainers and washed thoroughly in D-PBS to remove the potential sources of non-synovial cell contamination. 2. Washed synovial biopsy fragments were minced into small tissue pieces (~1 mm3) using a scalpel. 3. Minced fragments were transferred to V-bottom falcon tubes containing a digestion mix (RPMI culture medium with 100 μg/ml Liberase™ TL (Roche) and 100 μg/ml DNase I (Roche)). 4. Tissues were then dissociated with a combination of enzymatic digestion (37°C for 30min, water bath) and mechanical disruption (16G syringe needle) under continuous stirring with a combination of tiny ball-shaped and cylinder-shaped magnetic stirrers. 5. The mechanical disruption was performed 15 minutes after enzymatic digestion start by gently passing the samples through a 16G syringe needle (10x). 6. Enzymatic digestion was stopped with RPMI, containing 10% FCS followed by filtering the cell suspension through 40um strainer. 7. Nondigested tissue fragments, remaining on the strainer, were gently massaged with the syringe plunger head, to release the remaining synovial cells into filtered cell suspension. Any remaining drops of cell suspension were collected from the bottom side of the strainer with a fresh pipette tip and added to the filtered cell suspension. Additional washes were introduced to minimize cell loss. 8. Red blood cells in dissociated synovial cell pellets were lysed using Red Cell Lysis buffer (Roche), according to the manufacturer's instructions and cells were washed with PBS. All washing steps and volumes of reaction mixes were optimized to minimize cell loss throughout the protocol. Single cell 3´protocol (10x Genomics), v3.0/v3.1
characteristics: description
characteristics: adult
characteristics: developmental stage
characteristics: arthritis
characteristics: disease
characteristics: 78
characteristics: individual
characteristics: Homo sapiens
characteristics: organism
characteristics: Homo sapiens
characteristics: organism
characteristics: synovial membrane
characteristics: organism part
characteristics: Homo sapiens
characteristics: scientific_name
characteristics: female
characteristics: sex
characteristics: Syn_Bio_078
characteristics: title