| attributes |
| strain |
MYN1 |
| collection_date |
2009-10-09 |
| isol_growth_condt |
10.1111/jeu.12102 |
| env_feature |
pond |
| biotic_relationship |
free living |
| description |
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. |
| samp_mat_process |
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. |
| bioproject_id |
PRJDB3528 |
| estimated_size |
1.35 Gb |
| project_name |
Genome- and transcriptome-analysis of the photosynthetic testate amoeba Paulinella micropora |
| sample_title |
P. micropora total genome |
| samp_collect_device |
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. |
| ploidy |
missing |
| propagation |
eukaryote: asexual |
| env_material |
missing |
| num_replicons |
missing |
| geo_loc_name |
Japan:Ibaraki, Tsukuba |
| trophic_level |
photoautotroph |
| env_biome |
fresh water |
| lat_lon |
36.0485 N 140.1190 E |
| biomaterial_provider |
Mami Nomura, Ken-ichiro Ishida, Graduate School of Life and Environmental Science, University of Tsukuba |
| sample_name |
P. micropora total genome |
|