characteristics.text: 0.903089986991944
characteristics.characteristic: CD25 measurement (log10)
characteristics.text: 2.49415459401844
characteristics.characteristic: CD26L measurement (log10)
characteristics.text: 1.14612803567824
characteristics.characteristic: CD44 measurement (log10)
characteristics.text: 0.845098040014257
characteristics.characteristic: CD69 measurement (log10)
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2018-06-25T17:02:46Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-09-06T13:04:24Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104284765
characteristics.characteristic: External Id
characteristics.text: Cancer Research UK Cambridge Institute University of Cambridge
characteristics.characteristic: INSDC center name
characteristics.text: 2018-06-25T17:02:46Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-09-06T13:04:24Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1909743
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-6051:ACR_GG_00258
characteristics.characteristic: Submitter Id
characteristics.text: 11.5
characteristics.unit: week
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: CD8-positive, alpha-beta T cell
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000625
characteristics.characteristic: cell type
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Freshly dissected spleens from OT-I Rag1-deficient mice were homogenized through a 70 µm filter. CD8+ T cells were separated by negative selection using the CD8a+ T Cell Isolation Kit, mouse (Miltenyi Biotec). Isolated naive CD8+ OT-I T cells were stained with proliferation dye eFluor 450 (eBioscience). 100,000 cells per well of 96-well round-bottom plates were stimulated with 1 µM peptide in 200 µL complete RPMI (RPMI 1640 with 10% FCS, L-glutamine, sodium pyruvate, penicillin-streptomycin, and beta-mercaptoethanol) with 20 ng/mL (≥100 U/mL) murine IL-2. After culture, cells were washed in PBS, blocked with FcR blocking antibody (clone 93, Biolegend) and stained with Zombie Aqua viability dye (Biolegend), anti-CD8 eVolve 655 (clone 53-6.7, eBioscience), anti-CD44 APC-eFluor780 or APC-FIRE750 (clone IM7, eBioscience or Biolegend, respectively), anti-CD62L PE (clone MEL-14, eBioscience), anti-CD25 Alexa Fluor 488 (clone PC61.5, eBioscience), and anti-CD69 APC (clone H1.2F3, eBioscience). Cells were sorted on a BD Influx (BD Biosciences), selecting live cells that expressed CD8 and that had not proliferated. We did not see proliferation at the time points we examined. Expression of all surface proteins was recorded for each indexed cell. Single cell preparation was adapted from Picelli et al (2014, Nat Protoc, 9:171). Cells were sorted into 96-well plates holding 4 µL of lysis buffer composed of 2.3 U SUPERase In RNase inhibitor (Thermo Fisher Scientific), 0.11 % (v/v) Triton X-100 (Sigma), 12.5 mM DTT (Thermo Fisher Scientific), and 2.5 mM dNTP mix (Thermo Fisher Scientific). cDNA synthesis and amplification were adapted from Picelli et al (2014, Nat Protoc, 9:171). 1 µL annealing mix containing ERCC RNA Spike-In Mix (Thermo Fisher Scientific) diluted 1 in 30,000,000 and 10 µM oligo-dT30VN (Sigma) was added to each well before reverse transcription with SuperScript II (Invitrogen). cDNA amplification was performed with 23 PCR cycles and the resulting PCR products purified with Ampure XP Beads (Agencourt) at a volume ratio of 0.7:1 beads:DNA. Libraries were prepared using the Nextera XT DNA Sample Preparation Kit and indexes from the Nextera XT Index Kit v2 Set A and Nextera XT Index Kit v2 Set D (Illumina). Each plate of libraries was pooled, cleaned with Ampure XP beads, and quantified using KAPA Library Quantification Kit (Roche). Equimolar quantities of libraries from each plate were combined for sequencing.
characteristics.characteristic: description
characteristics.text: normal
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000461
characteristics.characteristic: disease
characteristics.text: OT-I; Rag1 knockout
characteristics.characteristic: genotype
characteristics.text: 2
characteristics.characteristic: individual
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_10090
characteristics.characteristic: organism
characteristics.text: spleen
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/BTO_0001281
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: female
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000383
characteristics.characteristic: sex
characteristics.text: ACR_GG_00258
characteristics.characteristic: single cell identifier
characteristics.text: OK
characteristics.characteristic: single cell well quality
characteristics.text: C57BL/6
characteristics.characteristic: strain
characteristics.text: ACR_GG_00258
characteristics.characteristic: title
characteristics.text: single cell
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009899
characteristics.characteristic: well information