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  • Open Access English
    Authors: 
    Campitelli, Laura F.; Yellan, Isaac; Albu, Mihai; Barazandeh, Marjan; Patel, Zain M.; Blanchette, Mathieu; Hughes, Timothy R.;
    Publisher: Zenodo
    Project: NSERC , CIHR

    Web Supplementary Files Web Supplementary File 1 - FASTA files containing full-length reconstruction input sequences: full_length_reconstruction_input_sequence_fastas.zip Web Supplementary File 2 - FASTA files containing Muscle alignments of the full-length reconstruction input sequences. full_length_reconstruction_input_sequence_alns.zip Web Supplementary File 3 - FASTA file of full-length reconstructed sequences: full_length_reconstructions.fa Web Supplementary File 4 - Table of full-length reconstruction statistics: full_length_reconstruction_stats.csv Web Supplementary File 5 - FASTA files containing ORF reconstruction input sequences: orf_fastas.zip Web Supplementary File 6 - FASTA files containing Macse alignments of the ORF reconstruction input sequences: ORF_reconstruction_input_sequence_alns.zip Web Supplementary File 7 - Table of ORF reconstruction statistics: ORF_reconstructions.fa Web Supplementary File 8 - Table of ORF reconstruction statistics: ORF_reconstruction_stats.csv Web Supplementary File 9 - Table of Composite Sequences: bestfl_selection_fixed_CS_seqs.csv Web Supplementary File 10 - Database of gold standards: L1_goldstandards.csv Data Underlying Figures RepeatMasker scans of hg38 and ancestral genomes: anc_gen_RM_out_files.zip Figure 4 4A Source alignment of 54 composite sequences: 220121_dropped12+L1ME3A_muscle.nt.afa Tree produced using the alignment and FastTree: 220121_dropped12+L1ME3A.tree 4B Source alignment of 67 Dfam L1 subfamily 3’ end models: 200123_dfam_3ends.fa.muscle.aln Tree produced using the alignment: 200123_dfam_3ends.fa.muscle.aln.tree Figure 5 KZFP-TE enrichment p-values (from Barazandeh et al 2018): TE_KZFP_enrichment_pvals.xlsx KZFP-TE top 500 peak overlap (from Barazandeh et al 2018): top500_peak_overlap.xlsx Figure 6 RepeatMasker .out file for the Composite Sequence custom library queried against hg38: CS_RM_hg38.fa.out.gz Figure S2 RepeatMasker scan .out file of hg38 (CG corrected Kimura Divergence values are in last column): hg38+KimDiv_RM.out RepeatMasker scan .out file of the Progressive Cactus eutherian ancestral genome (CG corrected Kimura Divergence values are in last column): Progressive_Cactus_Euth+KimDiv_RM.out RepeatMasker scan .out file of the Ancestors 1.1 eutherian ancestral genome (CG corrected Kimura Divergence values are in last column): Ancestors_Euth+KimDiv_RM.out Figure S5 RepeatMasker scan .out files for Progressive Cactus simian and primate reconstructed ancestral genomes: progCactus_RM_outfiles.zip S5A FASTA files containing Cactus genome-derived reconstructed sequences equivalent to the L1MA2, L1MA4, and L1MD1-3 best full-length sequences: progCactus_reconstruction_bestFL_equivalents.zip S5B FASTA files containing Muscle alignments of Cactus genome-derived full-length reconstruction input sequences: progCactus_reconstruction_input_sequence_alns.zip Figure S6 S6A Results of Conserved Domain scans of Cactus genome-derived full-length reconstructed sequences: CD_search_results_short_nms.txt S6B-D Character posterior probabilities of “best” full-length reconstructed sequences: best_fl_post_probs.zip Figure S7 S7B-C Results of Conserved Domain scans of translated initial full-length reconstructed sequences: initial_recons_all_3frametrans_CD-search.txt Results of Conserved Domain scans of translated reconstructed ORFs: recons_ORF1-2_all_3frametrans_CD-search.csv Figure S15 S15A Source alignment of 67 composite sequences: bestfl_selection_fixed_CS_seqs_muscle.nt.afa Tree produced using the alignment: bestfl_selection_fixed_CS_seqs_muscle.nt.afa.tree S15B-E Source Muscle alignments for phylogenetic trees of reconstructed sequence components: ORF2: ORF2_keep54_muscle.nt.afa 5’ UTR: 5utr_keep54_muscle.nt.afa ORF1: ORF1_keep54_muscle.nt.afa 3’ UTR: 3utr_keep54_muscle.nt.afa Trees produced using above alignments: ORF2: ORF2_keep54_muscle.nt.afa.tree 5’ UTR: 5utr_keep54_muscle.nt.afa.tree ORF1: ORF1_keep54_muscle.nt.afa.tree 3’ UTR: 3utr_keep54_muscle.nt.afa.tree Figure S17 Unfiltered BLAST results of Composite Sequences queried against hg38: CS_hg38_blastn.csv.zip BED file of L1 instances annotated using BLAST pipeline: BLAST_L1_hits.bed

  • Open Access
    Authors: 
    Fudge, Neva J.; Mearow, Karen M.;
    Publisher: Dryad
    Project: NSERC , CIHR

    Background: In our previous investigations of the role of the extracellular matrix (ECM) in promoting neurite growth we have observed that a permissive laminin (LN) substrate stimulates differential growth responses in subpopulations of mature dorsal root ganglion (DRG) neurons. DRG neurons expressing Trk and p75 receptors grow neurites on a LN substrate in the absence of neurotrophins, while isolectin B4-binding neurons (IB4+) do not display significant growth under the same conditions. We set out to determine whether there was an expression signature of the LN-induced neurite growth phenotype. Using a lectin binding protocol IB4+ neurons were isolated from dissociated DRG neurons, creating two groups - IB4+ and IB4-. A small-scale microarray approach was employed to screen the expression of a panel of ECM-associated genes following dissociation (t=0) and after 24 hr culture on LN (t=24LN). This was followed by qRT-PCR and immunocytochemistry of selected genes. Results: The microarray screen showed that 36 of the 144 genes on the arrays were consistently expressed by the neurons. The array analyses showed that six genes had lower expression in the IB4+ neurons compared to the IB4- cells at t=0 (CTSH, Icam1, Itgβ1, Lamb1, Plat, Spp1), and one gene was expressed at higher levels in the IB4+ cells (Plaur). qRT-PCR was carried out as an independent assessment of the array results. There were discrepancies between the two methods, with qRT-PCR confirming the differences in Lamb1, Plat and Plaur, and showing decreased expression of AdamTs1, FN, and Icam in the IB4+ cells at t=0. After 24 hr culture on LN, there were no significant differences detected by qRT-PCR between the IB4+ and IB4- cells. However, both groups showed upregulation of Itgβ1 and Plaur after 24 hr on LN, the IB4+ group also had increased Plat, and the IB4- cells showed decreased Lamb1, Icam1 and AdamTs1. Further, the array screen also detected a number of genes (not subjected to qRT-PCR) expressed similarly by both populations in relatively high levels but not detectably influenced by time in culture (Bsg, Cst3, Ctsb, Ctsd, Ctsl, Mmp14, Mmp19, Sparc. We carried out immunohistochemistry to confirm expression of proteins encoded by a number of these genes. Conclusions:Our results show that 1B4+ and IB4- neurons differ in the expression of several genes that are associated with responsiveness to the ECM prior to culturing (AdamTs1, FN, Icam1, Lamb1, Plat, Plaur). The data suggest that the genes expressed at higher levels in the IB4- neurons could contribute to the initial growth response of these cells in a permissive environment and could also represent a common injury response that subsequently promotes axon regeneration. The differential expression of several extracellular matrix molecules (FN, Lamb1, Icam) may suggest that the IB4- neurons are capable of maintaining /secreting their local extracellular environment which could aid in the regenerative process. Overall, these data provide new information on potential targets that could be manipulated to enhance axonal regeneration in the mature nervous system.

  • Open Access English

    OV2295 Tables ov2295_breakpoint_counts.csv.gz: Table of breakpoint counts per cell prediction_id: identifier for the breakpoint cell_id: identifier for the cell read_count: number of reads library_id: identifier for the DNA library sample_id: identifier for the sequenced sample chromosome_1: chromosome of breakend 1 strand_1: orientation of break end 1 position_1: position of break end 1 chromosome_2: chromosome of breakend 2 strand_2: orientation of break end 2 position_2: position of break end 2 ov2295_cell_cn.csv.gz: Table of cell specific copy number cell_id: identifier for the cell sample_id: identifier for the sequenced sample library_id: identifier for the DNA library chr: chromosome of bin start: start of bin end: end of bin reads: number of reads copy: raw normalized copy number state: copy number state gc: percent gc of the bin map: average mappability of the bin ov2295_cell_metrics.csv.gz: Table of cell metrics cell_id: identifier of the cell unpaired_mapped_reads: number of unpaired mapped reads paired_mapped_reads: number of mapped reads that were properly paired unpaired_duplicate_reads: number of unpaired duplicated reads paired_duplicate_reads: number of paired reads that were also marked as duplicate unmapped_reads: number of unmapped reads percent_duplicate_reads: percentage of duplicate reads estimated_library_size: scaled total number of mapped reads total_reads: total number of reads, regardless of mapping status total_mapped_reads: total number of mapped reads total_duplicate_reads: number of duplicate reads total_properly_paired: number of properly paired reads coverage_breadth: percentage of genome covered by some read coverage_depth: average reads per nucleotide position in the genome median_insert_size: median insert size between paired reads mean_insert_size: mean insert size between paired reads standard_deviation_insert_size: standard deviation of the insert size between paired reads index_sequence: index sequence of the adaptor sequence column: column of the cell on the nanowell chip img_col: column of the cell from the perspective of the microscope index_i5: id of the i5 index adapter sequence sample_type: type of the sample primer_i7: id of the i5 index primer sequence experimental_condition: experimental treatment of the cell, includes controls index_i7: id of the i7 index adapter sequence cell_call: living/dead classification of the cell based on staining usually, C1 == living, C2 == dead sample_id: name of the sample primer_i5: id of the i5 index primer sequence row: row of the cell on the nanowell chip library_id: identifier for the DNA library index: ignored multiplier: during parameter searching, the set [1..6] that was chosen MSRSI_non_integerness: median of segment residuals from segment integer copy number states MBRSI_dispersion_non_integerness: median of bin residuals from segment integer copy number states MBRSM_dispersion: median of bin residuals from segment median copy number values autocorrelation_hmmcopy: hmmcopy copy autocorrelation cv_hmmcopy: ignored empty_bins_hmmcopy: number of empty bins in hmmcopy mad_hmmcopy: median absolute deviation of hmmcopy copy mean_hmmcopy_reads_per_bin: mean reads per hmmcopy bin median_hmmcopy_reads_per_bin: median reads per hmmcopy bin std_hmmcopy_reads_per_bin: standard deviation value of reads in hmmcopy bins total_halfiness: summed halfiness penality score of the cell total_mapped_reads_hmmcopy: total mapped reads in all hmmcopy bins scaled_halfiness: summed scaled halfiness penalty score of the cell mean_state_mads: mean value for all median absolute deviation scores for each state mean_state_vars: variance value for all median absolute deviation scores for each state mad_neutral_state: median absolute deviation score of the neutral 2 copy state breakpoints: number of breakpoints, as indicated by state changes not at the ends of chromosomes mean_copy: mean hmmcopy copy value state_mode: the most commonly occuring state log_likelihood: hmmcopy log likelihood for the cell true_multiplier: the exact decimal value used to scale the copy number for segmentation order: order of the cell in the hierarchical clustering tree quality: random forest classifier proability score that cell is good ov2295_clone_alleles.csv.gz: Table of clone specific allele data chr: chromosome of bin start: start of bin end: end of bin hap_label: haplotype block identifier clone_id: clone identifier allele_1_sum: number of reads for allele 1 of the haplotype block allele_2_sum: number of reads for allele 2 of the haplotype block total_counts_sum: total reads for the haplotype block ov2295_clone_breakpoints.csv.gz: Table of breakpoints per clone for OV2295 samples. Columns: prediction_id: identifier for the breakpoint chromosome_1: chromosome of breakend 1 strand_1: orientation of break end 1 position_1: position of break end 1 chromosome_2: chromosome of breakend 2 strand_2: orientation of break end 2 position_2: position of break end 2 clone_id: clone identifier read_count: number of reads is_present: presence=1, absent=0 ov2295_clone_clusters.csv.gz: Table of cell clusters as putative clones cell_id: identifier for the cell clone_id: clone identifier ov2295_clone_cn.csv.gz: Table of allele specific copy number per clone for OV2295 samples. Columns: chr: chromosome of bin start: start of bin end: end of bin total_cn: HMMCopy predicted total copy number minor_cn: HMM predicted minor copy number major_cn: HMM predicted major copy number clone_id: clone identifier ov2295_clone_snvs.csv.gz: Table of SNVs per clone for OV2295 samples. Columns: chrom: chromosome coord: genome position ref: reference nucleotide alt: alternate nucleotide clone_id: clone identifier ref_counts: number of reads at this position matching the reference nucleotide alt_counts: number of reads at this position matching the alternate nucleotide total_counts: total number of reads at this position is_present: presence=0, absent=1 is_het: is heterozygous is_hom: is homozygous for the alternate ov2295_nodes.csv.gz: Table of phylogenetic information for SNV evolution variant_id: identifier for the SNV as chrom:coord:ref:alt node: node in the phylogenetic tree loss: probability the SNV was lost at this node origin: probability the SNV originated at this node presence: probability the SNV is present at this node ml_origin: binary indicator the SNV originated at this node ml_presence: binary indicator the SNV is present at this node ml_loss: binary indicator the SNV was lost at this node ov2295_snv_counts.csv.gz: Table of SNV counts chrom: chromosome coord: genome position ref: reference nucleotide alt: alternate nucleotide ref_counts: number of reads at this position matching the reference nucleotide alt_counts: number of reads at this position matching the alternate nucleotide cell_id: identifier for the cell total_counts: total number of reads at this position sample_id: identifier for the sequenced sample ov2295_tree.pickle: Phylogenetic tree in python pickle format. Requires installation of the stochastic dollo code at: https://bitbucket.org/dranew/dollo, version 0.4.2. Note the following sample mapping: ‘SA922’: ‘OV2295(R2)’, ‘SA921’: ‘TOV2295(R)’, ‘SA1090’: ‘OV2295’, Plots ov_supp_clone_allele_cn.png: Clone allele ratios for each OV2295 sample. ov_supp_clone_total_cn.png: Clone copy number for each OV2295 sample. ov_supp_sample_total_cn.png: Bulk copy number for each OV2295 sample. ov_supp_sample_allele_cn.png: Bulk allele ratios for each OV2295 sample.

  • Open Access
    Authors: 
    Madan, Christopher;
    Publisher: Zenodo
    Project: CIHR

    Surface meshes (.ply) from FreeSurfer subject 'bert'.

  • Open Access
    Authors: 
    Regev, Mor;
    Publisher: Zenodo
    Project: CIHR

    Six instrumental melodies composed by Joe Hisaishi, used as stimuli in the paper "Mapping the contents of consciousness during musical imagery"

  • Restricted
    Authors: 
    Magri, Stefania; Daniela, Di Bella; Taroni, Franco;
    Publisher: Zenodo
    Project: CIHR

    Next Generation Sequencing data of leukodystrophy gene panel analysis and segregation study data Sudy supported by Italian Ministry of Health. Grant Numbers: GR2016_02363337, RF2016_02361285

  • Research data . 2020
    Open Access English
    Authors: 
    Kondic, Todor; Schymanski, Emma;
    Publisher: Zenodo
    Project: CIHR

    This is a local CSV file of ECMDB 2.0 (http://ecmdb.ca/) for MetFrag (https://msbi.ipb-halle.de/MetFrag/). Data was extracted to CSV from the SDF, with column headers for compulsory fields adjusted to fit the MetFrag format. This file is for users wanting to integrate the latest ECMDB into MetFrag CL workflows (offline), this file will be integrated into MetFrag online; please use the file in the dropdown menu rather than uploading this one. The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Anyone using this resource should also cite the original publications from the Wishart Lab: (1) Sajed, T., Marcu, A., Ramirez, M., Pon, A., Guo, A., Knox, C., Wilson, M., Grant, J., Djoumbou, Y. and Wishart, D. (2015). ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res, p.gkv1060. PMID: 26481353. (2) ECMDB: The E. coli Metabolome Database. Guo AC, Jewison T, Wilson M, Liu Y, Knox C, Djoumbou Y, Lo P, Mandal R, Krishnamurthy R, Wishart DS. Nucleic Acids Res. 2012 Jan;41(Database issue):D625-30. PMID: 23109553

  • Research data . 2019
    Open Access English
    Authors: 
    Kondic, Todor; Schymanski, Emma;
    Publisher: Zenodo
    Project: CIHR

    This is a local CSV file of YMDB 2.0 (http://www.ymdb.ca/) for MetFrag (https://msbi.ipb-halle.de/MetFrag/). Data was extracted to CSV from the SDF, with column headers for compulsory fields adjusted to fit the MetFrag format. One entry with no SMILES was filled in using the InChI in OpenBabel; entries with no monoisotopic mass or formula were filled in using functions in RChemMass (https://github.com/schymane/RChemMass/), finally one generic formula (row 746) was replaced with the formula from the InChI. This file is for users wanting to integrate the latest YMDB into MetFrag CL workflows (offline), this file will be integrated into MetFrag online; please use the file in the dropdown menu rather than uploading this one. Anyone using this resource should also cite the original publications from the Wishart Lab: YMDB 2.0: A Significantly Expanded Version of the Yeast Metabolome Database. Ramirez-Guana M, Marcu A, Pon A, Guo AC, Sajed T, Wishart NA, Karu N, Djoumbou Y, Arndt D and Wishart DS. Nucleic Acids Res. 2017 Jan 4;45(D1):D440-D445. PubMed: 27899612 YMDB: The Yeast Metabolome Database. Jewison T, Neveu V, Lee J, Knox C, Liu P, Mandal R, Murthy RK, Sinelnikov I, Guo AC, Wilson M, Djoumbou Y and Wishart DS. Nucleic Acids Res. 2012 Jan;40(Database ussue):D815-20. PubMed: 22064855

  • Open Access
    Authors: 
    Strullu-Derrien, Christine; Bernard, S.; Spencer, Alan R.T.; Remusat, L.; Kenrick, Paul; Derrien, D.;
    Publisher: Zenodo
    Project: NSERC , CIHR , ANR | BCDiv (ANR-10-LABX-0003)

    Includes: 1) Propagation phase contrast X-ray synchrotron microtomography (PPC-SRμCT) dataset to study the three-dimensional structure of the permineralized wood from Armoricaphyton chateaupannense, using the ID19 beamline of the European Synchrotron Radiation Facility (ESRF), Grenoble, France. Dataset Information (also see scan_log.xml): Number of image in dataset: 2159 images Images prefix: plante_ Image x/y size: 3763 x 2048 px Image type: 16-bit TIFFs (with Pack Bits compression) Image size on disk: 14.8 MB each Scan date: 31-Oct-2008 Scan energy: 30keV Voxels size: 0.551 um Filters: Al_1_mm Al_0.5_mm Diam_U Projection number: 4000 Projection rotation: 360 degs Magnification: x20 Source-sample distance: 145000 Scan type: continuous Note: these images have been cropped from their original scan output size. 2) Two supplemental videos of the 3D model.

  • Research data . 2019
    Open Access English
    Authors: 
    Kondic, Todor; Schymanski, Emma;
    Publisher: Zenodo
    Project: CIHR

    This is a local CSV file of HMDB4.0 (http://www.hmdb.ca/) for MetFrag (https://msbi.ipb-halle.de/MetFrag/). Data was extracted from the XML, metals and entries with no monoisotopic mass were removed, one naming error for http://www.hmdb.ca/metabolites/HMDB0037436 was fixed and the XML fields adjusted to headers for MetFrag import. This file is for users wanting to integrate the latest HMDB into MetFrag CL workflows (offline), this file will be integrated into MetFrag online; please use the file in the dropdown menu rather than uploading this one. The two versions are identical, the two names fit various formatting conventions used behind the scenes in MetFragWeb.

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Include:
The following results are related to Canada. Are you interested to view more results? Visit OpenAIRE - Explore.
14 Research products, page 1 of 2
  • Open Access English
    Authors: 
    Campitelli, Laura F.; Yellan, Isaac; Albu, Mihai; Barazandeh, Marjan; Patel, Zain M.; Blanchette, Mathieu; Hughes, Timothy R.;
    Publisher: Zenodo
    Project: NSERC , CIHR

    Web Supplementary Files Web Supplementary File 1 - FASTA files containing full-length reconstruction input sequences: full_length_reconstruction_input_sequence_fastas.zip Web Supplementary File 2 - FASTA files containing Muscle alignments of the full-length reconstruction input sequences. full_length_reconstruction_input_sequence_alns.zip Web Supplementary File 3 - FASTA file of full-length reconstructed sequences: full_length_reconstructions.fa Web Supplementary File 4 - Table of full-length reconstruction statistics: full_length_reconstruction_stats.csv Web Supplementary File 5 - FASTA files containing ORF reconstruction input sequences: orf_fastas.zip Web Supplementary File 6 - FASTA files containing Macse alignments of the ORF reconstruction input sequences: ORF_reconstruction_input_sequence_alns.zip Web Supplementary File 7 - Table of ORF reconstruction statistics: ORF_reconstructions.fa Web Supplementary File 8 - Table of ORF reconstruction statistics: ORF_reconstruction_stats.csv Web Supplementary File 9 - Table of Composite Sequences: bestfl_selection_fixed_CS_seqs.csv Web Supplementary File 10 - Database of gold standards: L1_goldstandards.csv Data Underlying Figures RepeatMasker scans of hg38 and ancestral genomes: anc_gen_RM_out_files.zip Figure 4 4A Source alignment of 54 composite sequences: 220121_dropped12+L1ME3A_muscle.nt.afa Tree produced using the alignment and FastTree: 220121_dropped12+L1ME3A.tree 4B Source alignment of 67 Dfam L1 subfamily 3’ end models: 200123_dfam_3ends.fa.muscle.aln Tree produced using the alignment: 200123_dfam_3ends.fa.muscle.aln.tree Figure 5 KZFP-TE enrichment p-values (from Barazandeh et al 2018): TE_KZFP_enrichment_pvals.xlsx KZFP-TE top 500 peak overlap (from Barazandeh et al 2018): top500_peak_overlap.xlsx Figure 6 RepeatMasker .out file for the Composite Sequence custom library queried against hg38: CS_RM_hg38.fa.out.gz Figure S2 RepeatMasker scan .out file of hg38 (CG corrected Kimura Divergence values are in last column): hg38+KimDiv_RM.out RepeatMasker scan .out file of the Progressive Cactus eutherian ancestral genome (CG corrected Kimura Divergence values are in last column): Progressive_Cactus_Euth+KimDiv_RM.out RepeatMasker scan .out file of the Ancestors 1.1 eutherian ancestral genome (CG corrected Kimura Divergence values are in last column): Ancestors_Euth+KimDiv_RM.out Figure S5 RepeatMasker scan .out files for Progressive Cactus simian and primate reconstructed ancestral genomes: progCactus_RM_outfiles.zip S5A FASTA files containing Cactus genome-derived reconstructed sequences equivalent to the L1MA2, L1MA4, and L1MD1-3 best full-length sequences: progCactus_reconstruction_bestFL_equivalents.zip S5B FASTA files containing Muscle alignments of Cactus genome-derived full-length reconstruction input sequences: progCactus_reconstruction_input_sequence_alns.zip Figure S6 S6A Results of Conserved Domain scans of Cactus genome-derived full-length reconstructed sequences: CD_search_results_short_nms.txt S6B-D Character posterior probabilities of “best” full-length reconstructed sequences: best_fl_post_probs.zip Figure S7 S7B-C Results of Conserved Domain scans of translated initial full-length reconstructed sequences: initial_recons_all_3frametrans_CD-search.txt Results of Conserved Domain scans of translated reconstructed ORFs: recons_ORF1-2_all_3frametrans_CD-search.csv Figure S15 S15A Source alignment of 67 composite sequences: bestfl_selection_fixed_CS_seqs_muscle.nt.afa Tree produced using the alignment: bestfl_selection_fixed_CS_seqs_muscle.nt.afa.tree S15B-E Source Muscle alignments for phylogenetic trees of reconstructed sequence components: ORF2: ORF2_keep54_muscle.nt.afa 5’ UTR: 5utr_keep54_muscle.nt.afa ORF1: ORF1_keep54_muscle.nt.afa 3’ UTR: 3utr_keep54_muscle.nt.afa Trees produced using above alignments: ORF2: ORF2_keep54_muscle.nt.afa.tree 5’ UTR: 5utr_keep54_muscle.nt.afa.tree ORF1: ORF1_keep54_muscle.nt.afa.tree 3’ UTR: 3utr_keep54_muscle.nt.afa.tree Figure S17 Unfiltered BLAST results of Composite Sequences queried against hg38: CS_hg38_blastn.csv.zip BED file of L1 instances annotated using BLAST pipeline: BLAST_L1_hits.bed

  • Open Access
    Authors: 
    Fudge, Neva J.; Mearow, Karen M.;
    Publisher: Dryad
    Project: NSERC , CIHR

    Background: In our previous investigations of the role of the extracellular matrix (ECM) in promoting neurite growth we have observed that a permissive laminin (LN) substrate stimulates differential growth responses in subpopulations of mature dorsal root ganglion (DRG) neurons. DRG neurons expressing Trk and p75 receptors grow neurites on a LN substrate in the absence of neurotrophins, while isolectin B4-binding neurons (IB4+) do not display significant growth under the same conditions. We set out to determine whether there was an expression signature of the LN-induced neurite growth phenotype. Using a lectin binding protocol IB4+ neurons were isolated from dissociated DRG neurons, creating two groups - IB4+ and IB4-. A small-scale microarray approach was employed to screen the expression of a panel of ECM-associated genes following dissociation (t=0) and after 24 hr culture on LN (t=24LN). This was followed by qRT-PCR and immunocytochemistry of selected genes. Results: The microarray screen showed that 36 of the 144 genes on the arrays were consistently expressed by the neurons. The array analyses showed that six genes had lower expression in the IB4+ neurons compared to the IB4- cells at t=0 (CTSH, Icam1, Itgβ1, Lamb1, Plat, Spp1), and one gene was expressed at higher levels in the IB4+ cells (Plaur). qRT-PCR was carried out as an independent assessment of the array results. There were discrepancies between the two methods, with qRT-PCR confirming the differences in Lamb1, Plat and Plaur, and showing decreased expression of AdamTs1, FN, and Icam in the IB4+ cells at t=0. After 24 hr culture on LN, there were no significant differences detected by qRT-PCR between the IB4+ and IB4- cells. However, both groups showed upregulation of Itgβ1 and Plaur after 24 hr on LN, the IB4+ group also had increased Plat, and the IB4- cells showed decreased Lamb1, Icam1 and AdamTs1. Further, the array screen also detected a number of genes (not subjected to qRT-PCR) expressed similarly by both populations in relatively high levels but not detectably influenced by time in culture (Bsg, Cst3, Ctsb, Ctsd, Ctsl, Mmp14, Mmp19, Sparc. We carried out immunohistochemistry to confirm expression of proteins encoded by a number of these genes. Conclusions:Our results show that 1B4+ and IB4- neurons differ in the expression of several genes that are associated with responsiveness to the ECM prior to culturing (AdamTs1, FN, Icam1, Lamb1, Plat, Plaur). The data suggest that the genes expressed at higher levels in the IB4- neurons could contribute to the initial growth response of these cells in a permissive environment and could also represent a common injury response that subsequently promotes axon regeneration. The differential expression of several extracellular matrix molecules (FN, Lamb1, Icam) may suggest that the IB4- neurons are capable of maintaining /secreting their local extracellular environment which could aid in the regenerative process. Overall, these data provide new information on potential targets that could be manipulated to enhance axonal regeneration in the mature nervous system.

  • Open Access English

    OV2295 Tables ov2295_breakpoint_counts.csv.gz: Table of breakpoint counts per cell prediction_id: identifier for the breakpoint cell_id: identifier for the cell read_count: number of reads library_id: identifier for the DNA library sample_id: identifier for the sequenced sample chromosome_1: chromosome of breakend 1 strand_1: orientation of break end 1 position_1: position of break end 1 chromosome_2: chromosome of breakend 2 strand_2: orientation of break end 2 position_2: position of break end 2 ov2295_cell_cn.csv.gz: Table of cell specific copy number cell_id: identifier for the cell sample_id: identifier for the sequenced sample library_id: identifier for the DNA library chr: chromosome of bin start: start of bin end: end of bin reads: number of reads copy: raw normalized copy number state: copy number state gc: percent gc of the bin map: average mappability of the bin ov2295_cell_metrics.csv.gz: Table of cell metrics cell_id: identifier of the cell unpaired_mapped_reads: number of unpaired mapped reads paired_mapped_reads: number of mapped reads that were properly paired unpaired_duplicate_reads: number of unpaired duplicated reads paired_duplicate_reads: number of paired reads that were also marked as duplicate unmapped_reads: number of unmapped reads percent_duplicate_reads: percentage of duplicate reads estimated_library_size: scaled total number of mapped reads total_reads: total number of reads, regardless of mapping status total_mapped_reads: total number of mapped reads total_duplicate_reads: number of duplicate reads total_properly_paired: number of properly paired reads coverage_breadth: percentage of genome covered by some read coverage_depth: average reads per nucleotide position in the genome median_insert_size: median insert size between paired reads mean_insert_size: mean insert size between paired reads standard_deviation_insert_size: standard deviation of the insert size between paired reads index_sequence: index sequence of the adaptor sequence column: column of the cell on the nanowell chip img_col: column of the cell from the perspective of the microscope index_i5: id of the i5 index adapter sequence sample_type: type of the sample primer_i7: id of the i5 index primer sequence experimental_condition: experimental treatment of the cell, includes controls index_i7: id of the i7 index adapter sequence cell_call: living/dead classification of the cell based on staining usually, C1 == living, C2 == dead sample_id: name of the sample primer_i5: id of the i5 index primer sequence row: row of the cell on the nanowell chip library_id: identifier for the DNA library index: ignored multiplier: during parameter searching, the set [1..6] that was chosen MSRSI_non_integerness: median of segment residuals from segment integer copy number states MBRSI_dispersion_non_integerness: median of bin residuals from segment integer copy number states MBRSM_dispersion: median of bin residuals from segment median copy number values autocorrelation_hmmcopy: hmmcopy copy autocorrelation cv_hmmcopy: ignored empty_bins_hmmcopy: number of empty bins in hmmcopy mad_hmmcopy: median absolute deviation of hmmcopy copy mean_hmmcopy_reads_per_bin: mean reads per hmmcopy bin median_hmmcopy_reads_per_bin: median reads per hmmcopy bin std_hmmcopy_reads_per_bin: standard deviation value of reads in hmmcopy bins total_halfiness: summed halfiness penality score of the cell total_mapped_reads_hmmcopy: total mapped reads in all hmmcopy bins scaled_halfiness: summed scaled halfiness penalty score of the cell mean_state_mads: mean value for all median absolute deviation scores for each state mean_state_vars: variance value for all median absolute deviation scores for each state mad_neutral_state: median absolute deviation score of the neutral 2 copy state breakpoints: number of breakpoints, as indicated by state changes not at the ends of chromosomes mean_copy: mean hmmcopy copy value state_mode: the most commonly occuring state log_likelihood: hmmcopy log likelihood for the cell true_multiplier: the exact decimal value used to scale the copy number for segmentation order: order of the cell in the hierarchical clustering tree quality: random forest classifier proability score that cell is good ov2295_clone_alleles.csv.gz: Table of clone specific allele data chr: chromosome of bin start: start of bin end: end of bin hap_label: haplotype block identifier clone_id: clone identifier allele_1_sum: number of reads for allele 1 of the haplotype block allele_2_sum: number of reads for allele 2 of the haplotype block total_counts_sum: total reads for the haplotype block ov2295_clone_breakpoints.csv.gz: Table of breakpoints per clone for OV2295 samples. Columns: prediction_id: identifier for the breakpoint chromosome_1: chromosome of breakend 1 strand_1: orientation of break end 1 position_1: position of break end 1 chromosome_2: chromosome of breakend 2 strand_2: orientation of break end 2 position_2: position of break end 2 clone_id: clone identifier read_count: number of reads is_present: presence=1, absent=0 ov2295_clone_clusters.csv.gz: Table of cell clusters as putative clones cell_id: identifier for the cell clone_id: clone identifier ov2295_clone_cn.csv.gz: Table of allele specific copy number per clone for OV2295 samples. Columns: chr: chromosome of bin start: start of bin end: end of bin total_cn: HMMCopy predicted total copy number minor_cn: HMM predicted minor copy number major_cn: HMM predicted major copy number clone_id: clone identifier ov2295_clone_snvs.csv.gz: Table of SNVs per clone for OV2295 samples. Columns: chrom: chromosome coord: genome position ref: reference nucleotide alt: alternate nucleotide clone_id: clone identifier ref_counts: number of reads at this position matching the reference nucleotide alt_counts: number of reads at this position matching the alternate nucleotide total_counts: total number of reads at this position is_present: presence=0, absent=1 is_het: is heterozygous is_hom: is homozygous for the alternate ov2295_nodes.csv.gz: Table of phylogenetic information for SNV evolution variant_id: identifier for the SNV as chrom:coord:ref:alt node: node in the phylogenetic tree loss: probability the SNV was lost at this node origin: probability the SNV originated at this node presence: probability the SNV is present at this node ml_origin: binary indicator the SNV originated at this node ml_presence: binary indicator the SNV is present at this node ml_loss: binary indicator the SNV was lost at this node ov2295_snv_counts.csv.gz: Table of SNV counts chrom: chromosome coord: genome position ref: reference nucleotide alt: alternate nucleotide ref_counts: number of reads at this position matching the reference nucleotide alt_counts: number of reads at this position matching the alternate nucleotide cell_id: identifier for the cell total_counts: total number of reads at this position sample_id: identifier for the sequenced sample ov2295_tree.pickle: Phylogenetic tree in python pickle format. Requires installation of the stochastic dollo code at: https://bitbucket.org/dranew/dollo, version 0.4.2. Note the following sample mapping: ‘SA922’: ‘OV2295(R2)’, ‘SA921’: ‘TOV2295(R)’, ‘SA1090’: ‘OV2295’, Plots ov_supp_clone_allele_cn.png: Clone allele ratios for each OV2295 sample. ov_supp_clone_total_cn.png: Clone copy number for each OV2295 sample. ov_supp_sample_total_cn.png: Bulk copy number for each OV2295 sample. ov_supp_sample_allele_cn.png: Bulk allele ratios for each OV2295 sample.

  • Open Access
    Authors: 
    Madan, Christopher;
    Publisher: Zenodo
    Project: CIHR

    Surface meshes (.ply) from FreeSurfer subject 'bert'.

  • Open Access
    Authors: 
    Regev, Mor;
    Publisher: Zenodo
    Project: CIHR

    Six instrumental melodies composed by Joe Hisaishi, used as stimuli in the paper "Mapping the contents of consciousness during musical imagery"

  • Restricted
    Authors: 
    Magri, Stefania; Daniela, Di Bella; Taroni, Franco;
    Publisher: Zenodo
    Project: CIHR

    Next Generation Sequencing data of leukodystrophy gene panel analysis and segregation study data Sudy supported by Italian Ministry of Health. Grant Numbers: GR2016_02363337, RF2016_02361285

  • Research data . 2020
    Open Access English
    Authors: 
    Kondic, Todor; Schymanski, Emma;
    Publisher: Zenodo
    Project: CIHR

    This is a local CSV file of ECMDB 2.0 (http://ecmdb.ca/) for MetFrag (https://msbi.ipb-halle.de/MetFrag/). Data was extracted to CSV from the SDF, with column headers for compulsory fields adjusted to fit the MetFrag format. This file is for users wanting to integrate the latest ECMDB into MetFrag CL workflows (offline), this file will be integrated into MetFrag online; please use the file in the dropdown menu rather than uploading this one. The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Anyone using this resource should also cite the original publications from the Wishart Lab: (1) Sajed, T., Marcu, A., Ramirez, M., Pon, A., Guo, A., Knox, C., Wilson, M., Grant, J., Djoumbou, Y. and Wishart, D. (2015). ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res, p.gkv1060. PMID: 26481353. (2) ECMDB: The E. coli Metabolome Database. Guo AC, Jewison T, Wilson M, Liu Y, Knox C, Djoumbou Y, Lo P, Mandal R, Krishnamurthy R, Wishart DS. Nucleic Acids Res. 2012 Jan;41(Database issue):D625-30. PMID: 23109553

  • Research data . 2019
    Open Access English
    Authors: 
    Kondic, Todor; Schymanski, Emma;
    Publisher: Zenodo
    Project: CIHR

    This is a local CSV file of YMDB 2.0 (http://www.ymdb.ca/) for MetFrag (https://msbi.ipb-halle.de/MetFrag/). Data was extracted to CSV from the SDF, with column headers for compulsory fields adjusted to fit the MetFrag format. One entry with no SMILES was filled in using the InChI in OpenBabel; entries with no monoisotopic mass or formula were filled in using functions in RChemMass (https://github.com/schymane/RChemMass/), finally one generic formula (row 746) was replaced with the formula from the InChI. This file is for users wanting to integrate the latest YMDB into MetFrag CL workflows (offline), this file will be integrated into MetFrag online; please use the file in the dropdown menu rather than uploading this one. Anyone using this resource should also cite the original publications from the Wishart Lab: YMDB 2.0: A Significantly Expanded Version of the Yeast Metabolome Database. Ramirez-Guana M, Marcu A, Pon A, Guo AC, Sajed T, Wishart NA, Karu N, Djoumbou Y, Arndt D and Wishart DS. Nucleic Acids Res. 2017 Jan 4;45(D1):D440-D445. PubMed: 27899612 YMDB: The Yeast Metabolome Database. Jewison T, Neveu V, Lee J, Knox C, Liu P, Mandal R, Murthy RK, Sinelnikov I, Guo AC, Wilson M, Djoumbou Y and Wishart DS. Nucleic Acids Res. 2012 Jan;40(Database ussue):D815-20. PubMed: 22064855

  • Open Access
    Authors: 
    Strullu-Derrien, Christine; Bernard, S.; Spencer, Alan R.T.; Remusat, L.; Kenrick, Paul; Derrien, D.;
    Publisher: Zenodo
    Project: NSERC , CIHR , ANR | BCDiv (ANR-10-LABX-0003)

    Includes: 1) Propagation phase contrast X-ray synchrotron microtomography (PPC-SRμCT) dataset to study the three-dimensional structure of the permineralized wood from Armoricaphyton chateaupannense, using the ID19 beamline of the European Synchrotron Radiation Facility (ESRF), Grenoble, France. Dataset Information (also see scan_log.xml): Number of image in dataset: 2159 images Images prefix: plante_ Image x/y size: 3763 x 2048 px Image type: 16-bit TIFFs (with Pack Bits compression) Image size on disk: 14.8 MB each Scan date: 31-Oct-2008 Scan energy: 30keV Voxels size: 0.551 um Filters: Al_1_mm Al_0.5_mm Diam_U Projection number: 4000 Projection rotation: 360 degs Magnification: x20 Source-sample distance: 145000 Scan type: continuous Note: these images have been cropped from their original scan output size. 2) Two supplemental videos of the 3D model.

  • Research data . 2019
    Open Access English
    Authors: 
    Kondic, Todor; Schymanski, Emma;
    Publisher: Zenodo
    Project: CIHR

    This is a local CSV file of HMDB4.0 (http://www.hmdb.ca/) for MetFrag (https://msbi.ipb-halle.de/MetFrag/). Data was extracted from the XML, metals and entries with no monoisotopic mass were removed, one naming error for http://www.hmdb.ca/metabolites/HMDB0037436 was fixed and the XML fields adjusted to headers for MetFrag import. This file is for users wanting to integrate the latest HMDB into MetFrag CL workflows (offline), this file will be integrated into MetFrag online; please use the file in the dropdown menu rather than uploading this one. The two versions are identical, the two names fit various formatting conventions used behind the scenes in MetFragWeb.