| sample name | P. micropora total genome |
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| biomaterial provider | Mami Nomura, Ken-ichiro Ishida, Graduate School of Life and Environmental Science, University of Tsukuba |
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| observed biotic relationship | free living |
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| collection date | 2009-10-09 |
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| broad-scale environmental context | fresh water |
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| local-scale environmental context | pond |
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| environmental medium | missing |
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| estimated size | 1.35 Gb |
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| geographic location | Japan:Ibaraki, Tsukuba |
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| isolation and growth condition | 10.1111/jeu.12102 |
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| latitude and longitude | 36.0485 N 140.1190 E |
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| number of replicons | missing |
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| ploidy | missing |
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| project name | Genome- and transcriptome-analysis of the photosynthetic testate amoeba Paulinella micropora |
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| propagation | eukaryote: asexual |
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| sample collection device or method | 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. |
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| sample material processing | 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. |
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| strain | MYN1 |
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| trophic level | photoautotroph |
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