Sbarrato_Supplementary_Fig1
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1 Sbarrato_Supplementary_Fig1 Supplementary Figure 1. Translatome analysis of CLL patients based on IGVH mutational status ) Profile for the translatome of unmutated IGVH CLL versus mutated IGVH CLL pa9ents. Processed translatome data (log2 ra9os for each gene averaged across pa9ents) were ploed for mutated IGVH CLL pa9ents (x axis) versus unmutated IGVH CLL pa9ents. Grey, red and blue dots represent gene values for unchanging, upregula9on and dowregula9on respec9vely. Red and blue doed line represent the limit for fold change equal to 2 and 0.5 respec9vely. Contour plot was superimposed to highlight general shape of translatome (dark lines). ) 4- way Venn Diagram represen9ng the overlap of significantly iden9fied genes for deregula9on between unmutated and mutated IGVH CLL pa9ents in the four different sta9s9cal tests used: RankProd, Limma- eayes, SM and est.
2 Sbarrato_Supplementary_Fig2 C Supplementary Figure 2. Translatome analysis of CLL patients versus CTRL cells. 4- way Venn Diagram represen9ng the overlap of significantly iden9fied genes for deregula9on between CLL pa9ents and CTRL cells in the four different sta9s9cal tests used: RankProd, Limma- eayes, SM and est. ) Network analysis for GO term Ribosome among the significant genes iden9fied in at least 3 out of four sta9s9cal tests. Colour gradient represents the expression level of the translatome for each gene. C) Enrichment of GO Terms Ribosome, Protein iosynthesis and Nucleolus among the significant genes iden9fied in at least 3 out of four sta9s9cal tests. Genes were ranked and ploed by fold change between CLL pa9ents and CTRL cells.
3 Sbarrato_Supplementary_Fig3 Supplementary Figure 3. Transcriptome analysis of two published datasets for CLL patients versus CD19+ or CD5+ cells Controls. ) GO term analysis of CLL Transcriptome for GO Terms Ribosome and Protein iosynthesis among all genes from published dataset Haslinger between CLL pa9ents and CD19+ CTRL cells 32. Genes were ranked and ploed by fold change between CLL pa9ents and CD19+ CTRL cells. ) GO term analysis of CLL Transcriptome for GO Terms Ribosome and Protein iosynthesis among all genes from published dataset Seifert between CLL pa9ents and CD5+ CTRL cells 57. Genes were ranked and ploed by fold change between CLL pa9ents and CD5+ CTRL cells.
4 Sbarrato_Supplementary_Fig4 M523D M598 C M604E D U635C E U668 F time course 1 1 Expression n=5 No sign difference Supplementary figure 4: expression in IgM stimulated CLL cells. CLL cells from five different pa9ents were incubated in the presence of coupled Dynabeads or an9bodies for the indicated 9me. Western blots were performed to show expression of ader 3, 6, 16, 24 and s (- E). expression was quan9fied and normalized to before expression was made rela9ve to bead incuba9on for each 9me point. (F) Graph represents expression following CR s9mula9on with bead expression for each 9me point set to 1, bars (±SEM) represent the mean expression, n=5 no significant difference.
5 Sbarrato_Supplementary_Fig5 PFS High Low time (days) Supplementary Figure 5. Correlation between dyskerin expression and progression free survival. Pa9ents were divided into two groups based on dyskerin expression (low dyskerin vs high dyskerin) as in Figure 6. Impact of dyskerin expression on progression free survival was generated using Kaplan Meyer approxima9on and significance was es9mated by Log- Rank p value.
Supplementary. properties of. network types. randomly sampled. subsets (75%
Supplementary Information Gene co-expression network analysis reveals common system-level prognostic genes across cancer types properties of Supplementary Figure 1 The robustness and overlap of prognostic
SUPPLEMENTARY FIGURES
SUPPLEMENTARY FIGURES Figure S1. Clinical significance of ZNF322A overexpression in Caucasian lung cancer patients. (A) Representative immunohistochemistry images of ZNF322A protein expression in tissue
Supplementary Figure 1: Features of IGLL5 Mutations in CLL: a) Representative IGV screenshot of first
Supplementary Figure 1: Features of IGLL5 Mutations in CLL: a) Representative IGV screenshot of first intron IGLL5 mutation depicting biallelic mutations. Red arrows highlight the presence of out of phase
ARTICLE RESEARCH. Macmillan Publishers Limited. All rights reserved
Extended Data Figure 6 Annotation of drivers based on clinical characteristics and co-occurrence patterns. a, Putative drivers affecting greater than 10 patients were assessed for enrichment in IGHV mutated
Comparison of open chromatin regions between dentate granule cells and other tissues and neural cell types.
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Supplementary Figures
Supplementary Figures Supplementary Figure 1 Characterization of stable expression of GlucB and sshbira in the CT26 cell line (a) Live cell imaging of stable CT26 cells expressing green fluorescent protein
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Nature Structural and Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Mutational analysis of the SA2-Scc1 interaction in vitro and in human cells. (a) Autoradiograph (top) and Coomassie stained gel (bottom) of 35 S-labeled Myc-SA2 proteins (input)
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Supplementary Figure 1 Illustration of the working of network-based SVM to confidently predict a new (and now confirmed) ASD gene. Gene CTNND2 s brain network neighborhood that enabled its prediction by
Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Design of isolated protein and RNC constructs, and homogeneity of purified RNCs. (a) Schematic depicting the design and nomenclature used for all the isolated proteins and RNCs used
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Supplemental Figure 1
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Supplementary Figure 1 Identification of IFN-γ-producing CD8 + and CD4 + T cells with naive phenotype by alternative gating and sample-processing strategies. a. Contour 5% probability plots show definition
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Supplementary Figure 1 Quantification of myelin fragments in the aging brain (a) Electron microscopy on corpus callosum is shown for a 18-month-old wild type mice. Myelin fragments (arrows) were detected
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DOI:.38/ncb3399 a b c d FSP DAPI 5mm mm 5mm 5mm e Correspond to melanoma in-situ Figure a DCT FSP- f MITF mm mm MlanaA melanoma in-situ DCT 5mm FSP- mm mm mm mm mm g melanoma in-situ MITF MlanaA mm mm
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Supplementary text Collectively, we were able to detect ~14,000 expressed genes with RPKM (reads per kilobase per million) > 1 or ~16,000 with RPKM > 0.1 in at least one cell type from oocyte to the morula
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Supplementary Figure 1 Analysis of DNA methylation in a cancer cohort based on Infinium 450K data. RnBeads was used to rediscover a clinically distinct subgroup of glioblastoma patients characterized by
a surface permeabilized
a surface permeabilized RAW 64.7 P388D1 J774 b CD11b + Ly-6G - Blood Monocytes WT Supplementary Figure 1. Cell surface expression on macrophages and DCs. (a) RAW64.7, P388D1, and J774 cells were subjected
Theta sequences are essential for internally generated hippocampal firing fields.
Theta sequences are essential for internally generated hippocampal firing fields. Yingxue Wang, Sandro Romani, Brian Lustig, Anthony Leonardo, Eva Pastalkova Supplementary Materials Supplementary Modeling