characteristics.text: SAMD00026529
characteristics.characteristic: External Id
characteristics.text: Kyoto Prefectural University
characteristics.characteristic: INSDC center name
characteristics.text: 2019-09-15T00:00:00Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-04-05T05:06:38Z
characteristics.characteristic: INSDC last update
characteristics.text: live
characteristics.characteristic: INSDC status
characteristics.text: MIGS.eu
characteristics.characteristic: NCBI submission model
characteristics.text: MIGS.eu.6.0
characteristics.characteristic: NCBI submission package
characteristics.text: Mami Nomura, Ken-ichiro Ishida, Graduate School of Life and Environmental Science, University of Tsukuba
characteristics.characteristic: biomaterial provider
characteristics.text: free living
characteristics.characteristic: biotic relationship
characteristics.text: 2009-10-09
characteristics.characteristic: collection date
characteristics.text: P. micropora MYN1 strain was cultured under 14 hours light /10 hours dark photoperiodic cycle at 25 degrees C in the modified Waris-H+Si medium. Light intensity was set at 30-40 microE m-2s-1.
characteristics.characteristic: description
characteristics.text: fresh water
characteristics.characteristic: env_broad_scale
characteristics.text: pond
characteristics.characteristic: env_local_scale
characteristics.text: 1.35 Gb
characteristics.characteristic: estimated size
characteristics.text: Japan:Ibaraki, Tsukuba
characteristics.characteristic: geo loc name
characteristics.text: 10.1111/jeu.12102
characteristics.characteristic: isol_growth_condt
characteristics.text: 36.0485 N 140.1190 E
characteristics.characteristic: lat lon
characteristics.text: Paulinella micropora
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_1928728
characteristics.characteristic: organism
characteristics.text: Genome- and transcriptome-analysis of the photosynthetic testate amoeba Paulinella micropora
characteristics.characteristic: project name
characteristics.text: eukaryote: asexual
characteristics.characteristic: propagation
characteristics.text: For total genomic DNA extraction, P. micropora cells were homogenized using a 30 micrometer clearance glass homogenizer (RD440911, Teraoka co., Ltd, Osaka, Japan) with homogenization buffer (20 mM Tris-HCl (pH7.6), 10 mM NaCl, 10 mM KCl, 2.5 mM EDTA, 250 mM sucrose, 0.1 mM spermine, 0.5 mM spermidine, 1 mM DTT). The homogenates were centrifuged at 1000 x g for 10 minutes at 4 degrees C, and the pellets were incubated in lysis buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% SDS, 100 microgram/ml proteinase K) at 55 degrees C for 2 hours, followed by phenol/chloroform extraction and alcohol precipitation to obtain total genomic DNA fraction.
characteristics.characteristic: samp mat process
characteristics.text: P. micropora cells were harvested by low-speed centrifugation (500 x g, 2 minutes) at 4 degrees C. The harvested cells were passed through miracloth (Merk Millipore, Darmstadt, Germany) and 20 micrometer mesh-filter (HD-20, Nippon Rikagaku kikai co. Ltd, Tokyo, Japan) to eliminate contaminating bacteria that were enriched in the dead P. micropora cell aggregates larger than 20 micrometer, and followed by the washing with 10 mM Tris-HCl (pH8.0) three times, and with 10 mM Tris-HCl (pH8.0) plus 10 mM EDTA six times. Next, to remove the cell debris smaller than 5 micrometer, the cells were trapped on 5 micrometer mesh-filter (PP-5n, Kyoshin Rikoh Inc, Tokyo, Japan) and washed with 5 ml TE buffer. The recovered cells were kept at -80 degrees C.
characteristics.characteristic: samp_collect_device
characteristics.text: P. micropora total genome
characteristics.characteristic: sample name
characteristics.text: MYN1
characteristics.characteristic: strain
characteristics.text: P. micropora total genome
characteristics.characteristic: title
characteristics.text: photoautotroph
characteristics.characteristic: trophic_level