Journal: iScience

Article Title: Flowtigs: Safety in flow decompositions for assembly graphs

doi: 10.1016/j.isci.2024.111208

Figure Lengend Snippet:

Article Snippet: Our experiments with real data were performed on the ZymoBIOMICS Gut Microbiome Standard dataset (henceforth referred to by Zymo), a microbial community that mimics the human gut microbiome.

Techniques: Software

Journal: Cell

Article Title: Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells.

doi: 10.1016/j.cell.2020.04.027

Figure Lengend Snippet: Figure 2. Metagenomic Sequencing Reveals Decreased Abundance of Bifidobacterial Species on the Ketogenic Diet in Our Human Cohort (A) Heatmap showing fold change of the 50 most abundant species, comparing the ketogenic diet (KD) to baseline diet (BD) stages across all 17 subjects in our human study. Bacterial species are ordered by the magnitude and direction of the average fold change, from the most negative (top) to positive (bottom). (B) The ketogenic diet results in consistent reductions in the abundance of bifidobacterial species in our human cohort. Each line connects paired samples between the two diet arms from each study subject for bifidobacterial species detected in a study subject’s gut microbiota. See also Table S2.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Hemin Sigma Cat #51280 Resazurin Sigma Cat #199303 TOS-propionate agar Sigma Cat #43314 DTT Spectrum Cat #40400120-1 HBSS Life Technologies Cat #14025126 EDTA Invitrogen Cat #AM9260G Fetal bovine serum, heat inactivated Life Technologies Cat #10438026 Dispase II Roche Cat #501003345 DnaseI Sigma Cat #10104159001 Collagenase VIII Sigma Cat #C2139 Percoll VWR Cat #89428-524 PMA Fisher Scientific Cat #AAJ63916MCR Ionomycyin Sigma Cat #I0634 Cell stimulation cocktail Fisher Scientific Cat #501129036 Golgi plug Fisher Scientific Cat #BDB555029 Fixation/Permeabilization Solution Kit Fisher Scientific Cat #BDB555028 Sodium Pyruvate Life Technologies Cat #11360070 Penicillin-Streptomycin Thermo Fisher Cat #15070063 MEM Non-Essential Amino Acids Life Technologies Cat #11140050 GlutaMAX GIBCO Cat #35050061 RMPI 1640 Fisher Scientific Cat #11875119 HEPES Fisher Scientific Cat #NC0734307 Ham’s F-10 medium Fisher Scientific (Corning) Cat #MT10070CV Collagenase type I Worthington Cat #NC9633623 Bovine serum albumin Fisher Scientific Cat #BP1600-100 Critical Commercial Assays LiquiColor b-Hydroxybutyrate Colorimetric Assay VWR (Stanbio) Cat #10152-474 ZymoBIOMICS 96 MagBead DNA Kit Zymo Research Cat #D4302 Deposited Data 16S rRNA and shotgun metagenomic sequencing data NCBI SRA PRJNA529487 Experimental Models: Organisms/Strains Mouse: C57BL6/J, germ-free UCSF Gnotobiotics N/A Software and Algorithms GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ FlowJo v10.6.1 TreeStar https://www.flowjo.com/ R v3.5.3 CRAN https://r-project.org DADA2 v1.8.0 Callahan et al., 2016 https://benjjneb.github.io/dada2/ PhILR v1.6.0 Silverman et al., 2017 https://github.com/jsilve24/philr Vegan v2.5-5 Dixon, 2003 https://cran.r-project.org/web/packages/ vegan/index.html Ape v5.3 Paradis et al., 2004 https://cran.r-project.org/web/packages/ ape/index.html DESeq2 v1.20.0 Love et al., 2014 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html lmerTest v3.1-0 Kuznetsova et al., 2017 https://cran.r-project.org/web/packages/ lmerTest/index.html (Continued on next page) ll Cell 181, 1263–1275.e1–e8, June 11, 2020 e2 Article

Techniques: Sequencing

Journal: European Journal of Human Genetics

Article Title: Primary brain calcification: an international study reporting novel variants and associated phenotypes

doi: 10.1038/s41431-018-0185-4

Figure Lengend Snippet: Details on SLC20A2 variants and phenotype of variant carriers

Article Snippet: Briefly, these criteria included prior identification as a PFBC-causing variant (reported in the literature, HGMD, Clinvar, and/or the PFBC variant database https://coppolalab.ucla.edu/lovd/genes ), allele frequency in population databases (gnomAD [ 25 ], http://gnomad.broadinstitute.org/ ), computational and predictive data (Polyphen2, SIFT, MutationTaster, and splicing predictions provided by the Alamut visual software (Interactive Biosoftware, Rouen, France)), functional studies (reported in the literature), and segregation data.

Techniques: Variant Assay, Mutagenesis, Computed Tomography

Journal: European Journal of Human Genetics

Article Title: Primary brain calcification: an international study reporting novel variants and associated phenotypes

doi: 10.1038/s41431-018-0185-4

Figure Lengend Snippet: Details on PDGFRB variants and phenotype of variant carriers

Article Snippet: Briefly, these criteria included prior identification as a PFBC-causing variant (reported in the literature, HGMD, Clinvar, and/or the PFBC variant database https://coppolalab.ucla.edu/lovd/genes ), allele frequency in population databases (gnomAD [ 25 ], http://gnomad.broadinstitute.org/ ), computational and predictive data (Polyphen2, SIFT, MutationTaster, and splicing predictions provided by the Alamut visual software (Interactive Biosoftware, Rouen, France)), functional studies (reported in the literature), and segregation data.

Techniques: Variant Assay, Mutagenesis, Computed Tomography

Journal: European Journal of Human Genetics

Article Title: Primary brain calcification: an international study reporting novel variants and associated phenotypes

doi: 10.1038/s41431-018-0185-4

Figure Lengend Snippet: Details on XPR1 variants and phenotype of variant carriers

Article Snippet: Briefly, these criteria included prior identification as a PFBC-causing variant (reported in the literature, HGMD, Clinvar, and/or the PFBC variant database https://coppolalab.ucla.edu/lovd/genes ), allele frequency in population databases (gnomAD [ 25 ], http://gnomad.broadinstitute.org/ ), computational and predictive data (Polyphen2, SIFT, MutationTaster, and splicing predictions provided by the Alamut visual software (Interactive Biosoftware, Rouen, France)), functional studies (reported in the literature), and segregation data.

Techniques: Variant Assay, Mutagenesis, Computed Tomography, Concentration Assay

Journal: European Journal of Human Genetics

Article Title: Primary brain calcification: an international study reporting novel variants and associated phenotypes

doi: 10.1038/s41431-018-0185-4

Figure Lengend Snippet: Details on PDGFB variants and phenotype of variant carriers

Article Snippet: Briefly, these criteria included prior identification as a PFBC-causing variant (reported in the literature, HGMD, Clinvar, and/or the PFBC variant database https://coppolalab.ucla.edu/lovd/genes ), allele frequency in population databases (gnomAD [ 25 ], http://gnomad.broadinstitute.org/ ), computational and predictive data (Polyphen2, SIFT, MutationTaster, and splicing predictions provided by the Alamut visual software (Interactive Biosoftware, Rouen, France)), functional studies (reported in the literature), and segregation data.

Techniques: Variant Assay, Mutagenesis, Computed Tomography