characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2017-09-24T17:01:55Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-08-10T17:44:01Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104209798
characteristics.characteristic: External Id
characteristics.text: Department of Computer Science and Applied Mathematics, Weizmann Institute of Science
characteristics.characteristic: INSDC center name
characteristics.text: 2017-09-24T17:01:55Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-08-10T17:44:01Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1868816
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5968:920
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: H1
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0003042
characteristics.characteristic: cell line
characteristics.text: embryonic stem cell
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0002322
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: Followed by ~2 weeks of growth, a single clone was selected and detached to enable selection and picking of single cells. For the cell picking procedure cells were treated as described in (Biezuner et al. Genome Research. 2016) with the exception that prior to picking to scWGA reactions, cells were detached and dissociated using 550 U/ml StemPro Accutase Cell Dissociation Reagent (Gibco), incubated for 6 minutes, pulled down, re-suspended in iMEFs Conditioned hESC medium (CM) and were spread over a 6cm non-adherent petri dish.At the day of the experiment, before cell treatment, in order to minimize contamination, a clean working environment was established: bench and pipettes were RNase and DNA decontaminated (RNase AWAY, Molecular BioProducts) and consumables (PCR plates, tubes, tips etc.), non-kit reagents (PCR grade water, buffers etc.) and pipettes were UV irradiated. Individual cells were picked and deposited in separated single wells in dedicated 96-well PCR plates (Axigen, each kit in a separate plate), containing the required reagent. All pickings were performed on the same clone and at the same day (besides GPHI-SC, which was performed a few days later due to technical reasons). 1µl of positive (100pg Hela genomic DNA, NEB) and negative (water) controls were added as templates to non-deposited reaction wells. Samples were directly processed by their appropriate scWGA protocol. All reagents were immediately or sequentially (depending on the protocol) added to the original picking well, without material transfer, to avoid material loss. H1 human ES cells (WA01) were obtained from the WiCell Research Institute (Madison, WI). In order to create single cell (SC) clones, SCs were picked and deposited in separated single 96 wells using an automated cell picking device (CellCelector, ALS). Cells were cultured and treated as described in (Biezuner et al. Genome Research. 2016) The following scWGA kits were used (Kit short in manuscript, Kit name, Cat. Number, WGA technique, Manufacturer): Ampli1, Ampli1 WGA Kit, WG 001 050 R02, Linker adapter PCR (LA-PCR), Silicon Biosystems MALBAC, MALBAC Single Cell WGA Kit, YK001B, Multiple Annealing and Looping Based Amplification Cycles (MALBAC), Yikon Genomics GenomePlex, GenomePlex Single Cell Whole Genome Amplification Kit (WGA4), WGA4, Degenerate oligonucleotide-primed PCR (DOP-PCR), Sigma PicoPlex, PicoPLEX WGA Kit, E2620S, displacement DOP-PCR (D-DOP-PCR), New England Biolabs (manufactured by Rubicon) GPHI-SC, illustra Single Cell GenomiPhi DNA Amplification Kit, 29-1081-07, Multiple Displacement amplification (MDA), GE Healthcare RepliG-SC, REPLI-g Single Cell Kit, 150345, MDA, Qiagen TruePrime, TruePrime Single Cell WGA kit, 350025, MDA, SYGNIS Targeted enrichment using Access Array (Fluidigm) using the protocol as described in (Biezuner et al. Genome Research. 2016.) Sequencing primers are described in manuscript Supplementary Table 1.
characteristics.characteristic: description
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: MALBAC
characteristics.characteristic: scWGA kit
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: 920
characteristics.characteristic: title