characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-04-13T20:00:04Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-04-13T20:00:04Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA112637715
characteristics.characteristic: External Id
characteristics.text: Laboratory of Molecular Infection Medicine Sweden (MIMS), Department of molecular biology, Umea university
characteristics.characteristic: INSDC center name
characteristics.text: 2023-04-13T20:00:04Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-04-13T20:00:04Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS14629695
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12632:atac_lib3
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: Tonsils were collected from 5 human donors scheduled for tonsillectomy. B cells were enriched using negative selection magnetic beads (EasySep Human B Cell Isolation kit, Stemcell technologies, #17954). They were then pooled to avoid batch effects, with an average viability per donor of 92% (S.D. 1.5%). Library construction using 10x Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle. Enriched B cells were washed in ice-cold ATAC-seq resuspension buffer (RSB, 10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2), spun down, and resuspended in 100 mL ATAC-seq lysis buffer (RSB plus 0.1% NP-40 and 0.1% Tween-20 (Thermo Fisher). Lysis was allowed to proceed on ice for 5 min, then 900 mL RSB was added before spinning down again and resuspending in 50 mL 1X Nuclei Resuspension Buffer (10x Genomics). To assess nuclei purity and integrity after lysis, nuclei were stained with Trypan Blue (15250061, Thermo Fisher Scientific), and DAPI (D1306, Thermo Fisher Scientific), according to manufacturer recommendation. If necessary, cell concentrations were adjusted to equal ratios (per donor) prior to starting single-cell GEM emulsion droplet generation with the ATAC-seq NextGEM kit (10x Genomics). Briefly, nuclei were incubated in a transposition mix. Transposed nuclei were then loaded into a Chromium Next GEM Chip J. 9.000 nuclei were loaded per lane, with a target recovery of 5.500 (doublet rate 4% - 4.8%). After GEM emulsion generation, reverse transcription, cDNA amplification and multiome sc library generation occurred, according to manufacturer specifications (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, CG000338 Rev A, 10x Genomics, September 2020).
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: tonsillitis
characteristics.characteristic: disease
characteristics.text: mixed
characteristics.characteristic: individual
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: tonsil
characteristics.characteristic: organism part
characteristics.text: 3
characteristics.characteristic: replicate
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.characteristic: sex
characteristics.text: atac_lib3
characteristics.characteristic: title