Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of 18S rRNA gene with a focus on Chlorophyta

<b>Supplementary data 1</b>. Mothur script for sequence analysis<br><b>Supp. data 2</b>. Fasta file of Chlorophyta OTUs for V4<br><b>Supp. data 3</b>. Fasta file of Chlorophyta OTUs for V9<br><b>Supp. data 4</b>. Chlorophyta OTUs for V4 with assignation and read abundance at the different stations (Excel file).<br><b>Supp. data 5</b>. Chlorophyta OTUs for V9 with assignation and read abundance at the different stations (Excel file).<br><b>Supp. data 6</b>. Top 10 BLAST hits against Genbank nr database for Chlorophyta V4 OTUs. Red lines correspond to OTUs badly assigned to non Chlorophyta and green corresponds to OTUs badly assigned to another Chlorophyta representative.<br><b>Supp. data 7</b>. Top 10 BLAST hits against Genbank nr database for Chlorophyta V9 OTUs. Red lines correspond to OTUs badly assigned to non Chlorophyta and green lines corresponds to OTUs badly assigned to another Chlorophyta representative.<br

Additional file 7: Table S5. of Diatom flagellar genes and their expression during sexual reproduction in Leptocylindrus danicus

List of GO terms that were over or under represented in the transcriptome of the species L. danicus and L. aporus. Comparison was made on Fischer excat test in Blast2GO and only GO terms that are significantly different are listed (p-value <0.05). (XLSX 179 kb

Additional file 8: Table S6. of Diatom flagellar genes and their expression during sexual reproduction in Leptocylindrus danicus

Comparative presence or absence of all flagellar genes in diatom species showing at least one IFT-A or IFT-B subcomplex transcripts. For an exhaustive list, see Table S7. (XLSX 14 kb

Relative abundance of NGS V4 Leptocylindraceae sequences at the six stations.

<p>Data for plankton samples were inferred from the surface cDNA results normalised over the total number of sequences obtained for the sample and the average of the three size fractions (mean relative frequency). Data for sediment samples were inferred from cDNA template based sequences (relative frequency).</p

Venn diagrams showing the number of site-specific and shared OTUs among the six sampling stations.

<p>(A) V4 at Naples, Oslo Fjord, Gijon and Blanes (B) V9 at Varna, Oslo Fjord, Naples and Roscoff (C) V9 at Oslo Fjord, Gijon, Blanes and Naples. Venn diagrams for V9 have been split into two figures to compare OTU distribution among the sequence-abundant stations Naples and Oslo and the other four stations.</p

Relative abundance of NGS V9 Leptocylindraceae sequences at the six stations.

<p>Data for plankton samples were inferred from the surface cDNA results normalised over the total number of sequences obtained for the sample and the average of the three size fractions (mean relative frequency). Data for sediment samples were inferred from cDNA template based sequences (relative frequency), with the exception of sediment samples from Naples 2009 and Varna 2010.</p

RAxML tree inferred from the alignment of 165 representative V9 sequences of leptocylindracean OTUs from the BioMarKs data, six leptocylindracean sequences from GenBank, and 96 reference sequences of bolidomonads, leptocylindraceans and other diatoms, utilizing the GTRGAMMA base substitution model and Hill Climbing algorithm.

<p><i>Bolidomonas pacifica</i> and <i>B. mediterranea</i> were designated as outgroups. All non-leptocylindracean sequences were pruned from the tree following tree construction (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103810#pone.0103810.s002" target="_blank">Figure S2</a> for tree with outgroups included). Bootstrap values were inferred from 100 distinct alternative runs and values <50 are deleted. OTU labels follow same principle as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103810#pone-0103810-g001" target="_blank">Figure 1</a>.</p

RAxML tree inferred from the alignment of 12 representative V4 sequences of leptocylindracean OTUs from the BioMarKs data, 46 leptocylindracean sequences from GenBank, and 134 reference sequences of bolidomonads, Leptocylindraceae and other diatoms, utilizing the GTRGAMMA base substitution model and Hill Climbing algorithm.

<p><i>Bolidomonas pacifica</i> and <i>B. mediterranea</i> were designated as outgroups. All non-leptocylindracean reference sequences were pruned from the tree following tree construction (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103810#pone.0103810.s001" target="_blank">Figure S1</a> for tree with outgroups included). Bootstrap values were inferred from 100 distinct alternative runs and values <50 are deleted. Each OTU is labelled as follows: the first letter denotes the first letter of the genus, the second letter, the first one of the species; the number denotes the cluster number (numbering starts from zero); the number after the underscore denotes the abundance of the OTU.</p

Distribution maps of Leptocylindraceae species inferred from NGS V4 and V9 sequences in the BioMarKs and GenBank datasets (blue dots), plus reliable microscopy images (red dots).

<p>Absence of finding in the BioMarKs dataset is represented by grey dots. Records for the microscopic observation reports of species presence are provided in supplementary material.</p

Additional file 2 of Extracellular matrix profiles determine risk and prognosis of the squamous cell carcinoma subtype of non-small cell lung carcinoma

Additional file 2: Table S1. Differentially Expressed Hallmark Pathways in ECM-High vs ECM-Low Tumors. Table S2. Differentially Expressed MSigDb C2 Pathways in ECM-High vs ECM-Low Tumors. Table S3. Ligand-Receptor Interactions in ECM-High vs ECM-Low Tumors