characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2018-05-08T17:02:10Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-09-20T09:49:26Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104312203
characteristics.characteristic: External Id
characteristics.text: EMBL - EBI & Wellcome Trust Sanger Institute
characteristics.characteristic: INSDC center name
characteristics.text: 2018-05-08T17:02:10Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-09-20T09:49:26Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1937181
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-6066:BR_2_unst_0h_125
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: fibroblast derived cell line
characteristics.characteristic: cell line
characteristics.text: fibroblast
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000057
characteristics.characteristic: cell type
characteristics.text: Norway rat
characteristics.characteristic: common name
characteristics.text: Protocols: Cells were sorted with Beckman Coulter MoFlo XDP into wells containing 2uL of Lysis Buffer (1:20 solution of RNase Inhibitor (Clontech, Cat Number 2313A) in 0.2% v/v Triton X-100 (Sigma-Aldrich, Cat Number T9284), spun down and immediately frozen at -80°. Human dermal fibroblasts were obtained from the HipSci consortium (http://www.hipsci.org/ (Streeter et al., 2017) (where they were used for creating iPSCs). These original cells were thawed to test for growth and viability and refrozen after 1-2 passages, so that all lines were in the same growth rate and proliferation conditions before the stimulation experiment. Non-human primate cells were extracted from skin tissues that were incubated for 2hrs with 0.5% collagense-A (Roche; 11088815001) after mechanical processing, and then filtered through 100m strainers before being plated and passaged prior to cryo-banking. Rodent cells were obtained from Cellbiologics where they were extracted using a similar enzymatic extraction protocol using skin tissues from the same regions of the body used in primates. Cell were grown in ATCC fibroblast growth medium (Fibroblast Basal Medium (ATCC, ATCC-PCS-201-030) with Fibroblast Growth Kit-Low serum (ATCC, PCS-201-041) Cells were stimulated with 1ug/mL of High-Molecular Weight poly I:C (Invivogen, Cat. Code: tlrl-pic), transfected with 2uL/mL Lipofectamin 2,000 , for 0,4,8 hours. Sorted plates were processed according to the Smart-seq2 protocol (Picelli et al., 2014): Oligo-dT primer (IDT), dNTPs (ThermoFisher, Cat Number 10319879) and ERCC RNA Spike-In Mix (1:25,000,000 final dilution, Ambion, Cat Number 4456740) were added to each well, and Reverse Transcription (using 50U SmartScribe, Clontech Cat Number 639538) and PCR were performed following the original protocol with 25 PCR cycles. cDNA libraries were prepared using Nextera XT DNA Sample Preparation Kit (Illumina, Cat Number FC-131-1096), according to the protocol supplied by Fluidigm (PN 100-5950 B1). Quality Checks on cDNA were done using a Bioanalyser 2100 (Agilent Technologies). Libraries from 96 single cells were quantified using the LightCycler 480 (Roche), pooled and purified using AMPure XP beads (Beckman Coulter) with Hamilton 384 head robot (Hamilton Robotics). Pooled samples were sequenced on an Illumina HiSeq 2500 instrument, using paired-end 125-bp reads.
characteristics.characteristic: description
characteristics.text: normal
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000461
characteristics.characteristic: disease
characteristics.text: 2
characteristics.characteristic: individual
characteristics.text: Rattus norvegicus
characteristics.characteristic: organism
characteristics.text: Rattus norvegicus
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_10116
characteristics.characteristic: organism
characteristics.text: dermis
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0002067
characteristics.characteristic: organism part
characteristics.text: Rattus norvegicus
characteristics.characteristic: scientific_name
characteristics.text: female
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000383
characteristics.characteristic: sex
characteristics.text: BN
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_10116
characteristics.characteristic: strain
characteristics.text: BR_2_unst_0h_125
characteristics.characteristic: title