第16回千葉カルシウム代謝研究会

Gene ontology term enrichments for RNA-Seq data from differentiated TSC2 deletion cell lines and microarray data of patient SEGAs (related to Fig. 2f). (XLSX 27.7 kb

Phylogenetic affiliation of clones within choanoflagellates.

<p>Maximum-likelihood phylogenetic tree constructed with 54 partial and complete choanoflagellate sequences (733 informative positions). Clades A–I follow the notation of del Campo and Massana <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041970#pone.0041970-delCampo1" target="_blank">[38]</a>. Four additional clades (J–M) are introduced. For further description see legend of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041970#pone-0041970-g006" target="_blank">Figure 6</a>.</p

Phylogenetic affiliation of clones within cercozoans.

<p>Maximum-likelihood phylogenetic tree constructed with 77 partial and complete cercozoan sequences (1059 informative positions). For further description see legend of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041970#pone-0041970-g006" target="_blank">Figure 6</a>.</p

Phylogenetic composition in clone libraries constructed from the three incubation experiments.

<p>Upper and middle panels show the composition of clones in the 3-µm filtered initial and final incubation samples, respectively. The unfiltered final incubation samples are represented by the lower panels. For each library, the proportion of clones within the major taxonomic groups is displayed as pie charts. A finer resolution of the taxonomic groups and their contribution to each library is shown in the bar charts.</p

Novelty pattern determined for all clones obtained at the start and end of incubation experiments.

<p>Each circle represents one clone and its percent similarity to the closest environmental clone and the closest cultured species in GenBank. The mean similarity to both is indicated by the squares.</p

Comparison of 18S rRNA fingerprints at the start and end of three incubation experiments.

<p>(A) Stacked bar chart showing the relative intensity of the sequenced gel bands in each lane from filtered and unfiltered samples taken at the start and end of the incubation within the three experiments. Each color of the stacked bars represents one band and the length corresponds to the relative band intensity. (B) Numbered arrows indicate sequenced bands in the inverted DGGE image. (C) Information on the phylogenetic affiliation and trophic functions of sequenced bands with the band numbers referring to the bands in the DGGE image and the color code referring to the stacked bars chart.</p

Community shift towards heterotrophic taxa revealed by assignment of trophic functions to 18S rRNA sequences.

<p>The proportion of sequences assigned a trophic function (phototroph, heterotroph, unknown) at the start and end of incubation, as determined in clone libraries (A) and DGGE analysis (B).</p

Cell number development in the course of three incubation experiments.

<p>(A) the abundance of total, high, and low nucleic acid containing bacteria (total, HNA, and LNA) for the 3-µm filtered and unfiltered treatments, respectively. (B) Cell numbers of <i>Synechococcus</i> (Syn), phototrophic eukaryotes (PE), and heterotrophic flagellates (HF) in the 3-µm filtered and unfiltered treatments. Error bars indicate the standard deviation in triplicate incubation bottles.</p

Additional file 8: Table S5. of Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model

Gene set enrichment analysis of ribosome profiling data (related to Fig. 3d). (XLSX 11.1 kb

Additional file 9: Table S6. of Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model

Gene ontology term enrichments for ribosome profiling data (related to Fig. 3f). (XLSX 11 kb