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MOESM6 of Central nervous system transcriptome of Biomphalaria alexandrina, an intermediate host for schistosomiasis

Tamer Mansour, Mohamed Habib, Laura Rodríguez, Anthony Vázquez, Julián Alers, Alfredo Ghezzi, Roger Croll, C. Brown & Mark Miller
Additional file 6. BLAST against B. glabrata: A reciprocal BLAST search against the recently published transcriptome of twelve pooled Biomphalaria glabrata tissues [3].

Additional file 2: of Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii

Musa A. Hassan, Juan Vasquez, Chew Guo-Liang, Markus Meissner & T. Nicolai Siegel
Dataset. A) Average DESeq2 normalized RNA-seq and Ribo-seq read counts for all the transcripts tested for differential expression and ribosome occupancy. B) Genes exhibiting low ribosome occupancy but above background mRNA abundance. C) Genes exhibiting low mRNA abundance but above background ribosome occupancy. D) Genes that are differentially regulated both at the level of mRNA abundance and ribosome occupancy (RNAâ +â RIBO). E) Genes that are differentially regulated only at the level of mRNA abundance...

MOESM5 of Central nervous system transcriptome of Biomphalaria alexandrina, an intermediate host for schistosomiasis

Tamer Mansour, Mohamed Habib, Laura Rodríguez, Anthony Vázquez, Julián Alers, Alfredo Ghezzi, Roger Croll, C. Brown & Mark Miller
Additional file 5. Hi-Express transcripts: Highly expressed transcripts annotated by the BLAST results against the comprehensive NCBI Non-Redundant (NR) database.

Additional file 1: of A simple and accurate rule-based modeling framework for simulation of autocrine/paracrine stimulation of glioblastoma cell motility and proliferation by L1CAM in 2-D culture

Justin Caccavale, David Fiumara, Michael Stapf, Liedeke Sweitzer, Hannah Anderson, Jonathan Gorky, Prasad Dhurjati & Deni Galileo
NetLogo file of the modeling framework described in this article that simulates autocrine/paracrine stimulation of glioblastoma cell motility and proliferation by L1CAM in 2-D culture. The NetLogo software can be downloaded at https://ccl.northwestern.edu/netlogo/ . (NLOGO 28 kb)

MOESM4 of Central nervous system transcriptome of Biomphalaria alexandrina, an intermediate host for schistosomiasis

Tamer Mansour, Mohamed Habib, Laura Rodríguez, Anthony Vázquez, Julián Alers, Alfredo Ghezzi, Roger Croll, C. Brown & Mark Miller
Additional file 4. Final assembly: Transcripts annotated with transcript length and expression level in TPM values. Also, if identified, transcripts were annotated by their orthologs. Otherwise, annotation was implemented using homologs or with possible open reading frames.

MOESM3 of Central nervous system transcriptome of Biomphalaria alexandrina, an intermediate host for schistosomiasis

Tamer Mansour, Mohamed Habib, Laura Rodríguez, Anthony Vázquez, Julián Alers, Alfredo Ghezzi, Roger Croll, C. Brown & Mark Miller
Additional file 3. Homologous Transcripts: Transcripts with significant one-way BLAST hits against the UniProtKB/Swiss-Prot database.

MOESM2 of Central nervous system transcriptome of Biomphalaria alexandrina, an intermediate host for schistosomiasis

Tamer Mansour, Mohamed Habib, Laura Rodríguez, Anthony Vázquez, Julián Alers, Alfredo Ghezzi, Roger Croll, C. Brown & Mark Miller
Additional file 2. Orthologous Transcripts: Transcripts with significant mutual BLAST hits against the UniProtKB/Swiss-Prot database.

MOESM1 of Central nervous system transcriptome of Biomphalaria alexandrina, an intermediate host for schistosomiasis

Tamer Mansour, Mohamed Habib, Laura Rodríguez, Anthony Vázquez, Julián Alers, Alfredo Ghezzi, Roger Croll, C. Brown & Mark Miller
Additional file 1. Coding Transcripts: Transcripts with long open reading frames (≥100 amino acids).

Additional file 1: of Indacaterol/glycopyrronium is cost-effective compared to salmeterol/fluticasone in COPD: FLAME-based modelling in a Swedish population

Leif Bjermer, Job Van Boven, Madlaina Costa-Scharplatz, Dorothy Keininger, Florian Gutzwiller, Karin Lisspers, Ronan Mahon, Petter Olsson & Nicolas Roche
Methods and Results (additional details) (ZIP 535 kb)

Additional file 1: Table S4. of Micro-structural bone changes in early rheumatoid arthritis persist over 1-year despite use of disease modifying anti-rheumatic drug therapy

Lynne Feehan, Linda Li & Heather McKay
HR-pQCT Time (Baseline vs 12-months) Main Effects Summary. Summary of data and statistical results for the Time main (Baseline vs 12-months) effect analyses. Table S5. HR-pQCT Interaction [Disease (RA vs NRA) x Time (Baseline vs 12-months)] Main Effects Summary. Summary of data and statistical results for the Interaction (Disease x Time) main effect analyses. (XLSX 22 kb)

Additional file 7: Table S6. of Impact of prematurity and nutrition on the developing gut microbiome and preterm infant growth

Alex Grier, Xing Qiu, Sanjukta Bandyopadhyay, Jeanne Holden-Wiltse, Haeja Kessler, Ann Gill, Brooke Hamilton, Heidie Huyck, Sara Misra, Thomas Mariani, Rita Ryan, Lori Scholer, Kristin Scheible, Yi-Horng Lee, Mary Caserta, Gloria Pryhuber & Steven Gill
Significant associations between bacterial taxa and nutrition, medications, and other clinical factors, within each of the three phases of the microbiome. (XLSX 34 kb)

Additional file 6: Table S5. of Impact of prematurity and nutrition on the developing gut microbiome and preterm infant growth

Alex Grier, Xing Qiu, Sanjukta Bandyopadhyay, Jeanne Holden-Wiltse, Haeja Kessler, Ann Gill, Brooke Hamilton, Heidie Huyck, Sara Misra, Thomas Mariani, Rita Ryan, Lori Scholer, Kristin Scheible, Yi-Horng Lee, Mary Caserta, Gloria Pryhuber & Steven Gill
Significant results of linear discriminant analysis of putative functional features of microbial communities across the three Phases of the microbiome. (XLSX 24 kb)

Additional file 9: Category 1. of The asymmetric cell division machinery in the spiral-cleaving egg and embryo of the marine annelid Platynereis dumerilii

Aron Nakama, Hsien-Chao Chou & Stephan Schneider
Cortical Domain genes. Individual developmental expression profiles for each ACD gene including standard deviation error bars for all time points are shown. (XLSX 88 kb)

Additional file 5: Table S4. of Impact of prematurity and nutrition on the developing gut microbiome and preterm infant growth

Alex Grier, Xing Qiu, Sanjukta Bandyopadhyay, Jeanne Holden-Wiltse, Haeja Kessler, Ann Gill, Brooke Hamilton, Heidie Huyck, Sara Misra, Thomas Mariani, Rita Ryan, Lori Scholer, Kristin Scheible, Yi-Horng Lee, Mary Caserta, Gloria Pryhuber & Steven Gill
A. Results of differential abundance tests (metagenomeSeq zero-inflated Gaussian) of all bacterial taxa between microbiome phases 1 and 2. B. Results of differential abundance tests (metagenomeSeq zero-inflated Gaussian) of all bacterial taxa between microbiome phases 2 and 3. C. Results of differential abundance tests (metagenomeSeq zero-inflated Gaussian) of all bacterial taxa between microbiome phases 1 and 3. (ZIP 536 kb)

Additional file 8: of The asymmetric cell division machinery in the spiral-cleaving egg and embryo of the marine annelid Platynereis dumerilii

Aron Nakama, Hsien-Chao Chou & Stephan Schneider
Gene Ontology Search Query: Cell Junction. List of all genes and expression profiles for time points 0â 14 hpf generated for a GO Search: Cell Junction (related to Figs. 5-7). Search hits are generated for the Biological Process GO category that contains a Cell Junction annotation. The table was organized by sorting the 2 hpf FPKM expression values from large-to-small. All values below 1 FPKM at 2 hpf were excluded. The expression profiles and the...

Additional file 4: Table S3. of Impact of prematurity and nutrition on the developing gut microbiome and preterm infant growth

Alex Grier, Xing Qiu, Sanjukta Bandyopadhyay, Jeanne Holden-Wiltse, Haeja Kessler, Ann Gill, Brooke Hamilton, Heidie Huyck, Sara Misra, Thomas Mariani, Rita Ryan, Lori Scholer, Kristin Scheible, Yi-Horng Lee, Mary Caserta, Gloria Pryhuber & Steven Gill
Kruskal-Wallis analysis of variance of all bacterial taxa across the three Phases of the microbiome. (XLSX 109 kb)

Additional file 7: of The asymmetric cell division machinery in the spiral-cleaving egg and embryo of the marine annelid Platynereis dumerilii

Aron Nakama, Hsien-Chao Chou & Stephan Schneider
Gene Ontology Search Query: Cell Adhesion. List of all genes and expression profiles for time points 0â 14 hpf generated for a GO Search: Cell Adhesion (related to Figs. 5-7). Search hits are generated for the Biological Process GO category that contains a Cell Adhesion annotation. The table was organized by sorting the 2 hpf FPKM expression values from large-to-small. All values below 1 FPKM at 2 hpf were excluded. The expression profiles and the...

Additional file 6: of The asymmetric cell division machinery in the spiral-cleaving egg and embryo of the marine annelid Platynereis dumerilii

Aron Nakama, Hsien-Chao Chou & Stephan Schneider
Gene Ontology Search Query: Cell Polarity Genes. List of all genes and expression profiles for time points 0â 14 hpf generated for a GO Search: Cell Polarity (related to Figs. 3-7). Search hits are generated for the Biological Process GO category that contains a Cell Polarity annotation. The table was organized by sorting the 2 hpf FPKM expression values from large-to-small. All values below 1 FPKM at 2 hpf were excluded. The expression profiles and...

Additional file 5: of The asymmetric cell division machinery in the spiral-cleaving egg and embryo of the marine annelid Platynereis dumerilii

Aron Nakama, Hsien-Chao Chou & Stephan Schneider
RNA-seq data for each ACD gene within the four categories during early development of P.dumerilii. Quantitative expression levels are shown as FPKM for each gene at two-hour time points from 2 to 14 hpf (related to Figs. 3-7). Independent measurements for two biological replicates of each embryonic stage and for technical replicates of eight samples are shown. Data can be found on the on Pdumbase http://pdumbase.gdcb.iastate.edu/platynereis/controller.php?action=home [63]. (XLSX 54 kb)

Additional file 10: Table S9. of Impact of prematurity and nutrition on the developing gut microbiome and preterm infant growth

Alex Grier, Xing Qiu, Sanjukta Bandyopadhyay, Jeanne Holden-Wiltse, Haeja Kessler, Ann Gill, Brooke Hamilton, Heidie Huyck, Sara Misra, Thomas Mariani, Rita Ryan, Lori Scholer, Kristin Scheible, Yi-Horng Lee, Mary Caserta, Gloria Pryhuber & Steven Gill
Linear regression analysis of significant taxa for two variables (genera in P1 and genera in meconium), those that are significant for both variables and those that are unique to each (P1 or meconium). (XLSX 9 kb)

Additional file 7: Table S7. of Mosaicism for structural non-centromeric autosomal rearrangement in prenatal diagnoses: evidence for sex-specific selection against chromosomal abnormalities

Natalia Kovaleva & Philip Cotter
Mosaicism for structural rearrangements in miscarried/spontaneously aborted fetuses. Tabular data presenting details of miscarried/spontaneously aborted fetuses with structural rearrangement: karyotype, parental ages, proportion of abnormal cell line(s), reasons for cytogenetic testing, and probality of maternal cell contamination in female specimens. (XLSX 8 kb)

Additional file 6: Table S6. of Mosaicism for structural non-centromeric autosomal rearrangement in prenatal diagnoses: evidence for sex-specific selection against chromosomal abnormalities

Natalia Kovaleva & Philip Cotter
Mosaicism for apparently balanced rearrangements. Tabular data presenting details of carriers of mosaicism for apparently balanced rearrangement: karyotype, parental ages, proportion of abnormal cell line(s), confirmation testing, indications for cytogenetic testing, outcome of the pregnancy. (XLSX 7 kb)

Additional file 5: Table S5. of Mosaicism for structural non-centromeric autosomal rearrangement in prenatal diagnoses: evidence for sex-specific selection against chromosomal abnormalities

Natalia Kovaleva & Philip Cotter
Mosaicism for other unbalanced rearrangements. Tabular data presenting details of carriers of mosaicism for other unbalanced rearrangement: karyotype, parental ages, proportion of abnormal cell line(s), confirmation testing, indications for cytogenetic testing, outcome of the pregnancy. (XLSX 6 kb)

Additional file 4: Table S4. of Mosaicism for structural non-centromeric autosomal rearrangement in prenatal diagnoses: evidence for sex-specific selection against chromosomal abnormalities

Natalia Kovaleva & Philip Cotter
Mosaicism for unbalanced translocations. Tabular data presenting details of carriers of mosaicism for unbalanced translocation: karyotype, parental ages, proportion of abnormal cell line(s), confirmation testing, indications for cytogenetic testing, outcome of the pregnancy. (XLSX 6 kb)

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