cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6891530
title: MOESM8 of Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis

description: Additional file 8. Analysis of differential gene expression comparison between short-term and long-term samples. Table presents the results of DESeq2 differential expression analysis comparing the group of short-term samples (goats 1â 3) and long-term samples (goats 4â 7). Data are sorted by the adjusted p-value for each comparison (Column G), from smallest to largest. Genes are identified by the locus tag in Column A. The log2FoldChange (Column C) indicates the log2 of the differential gene expression of (Long-term/Short-term) samples.
DOI: 10.7910/dvn/debtui/mx9ck5
title: 0V

description: sigma=0volts
DOI: 10.6084/m9.figshare.6891530.v1
title: MOESM8 of Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis

description: Additional file 8. Analysis of differential gene expression comparison between short-term and long-term samples. Table presents the results of DESeq2 differential expression analysis comparing the group of short-term samples (goats 1â 3) and long-term samples (goats 4â 7). Data are sorted by the adjusted p-value for each comparison (Column G), from smallest to largest. Genes are identified by the locus tag in Column A. The log2FoldChange (Column C) indicates the log2 of the differential gene expression of (Long-term/Short-term) samples.
DOI: 10.7910/dvn/debtui/nrqbu7
title: 0V

description: sigma=0volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/yoj0c7
title: 0V

description: sigma=0volts
DOI: 10.6084/m9.figshare.6891518
title: MOESM7 of Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis

description: Additional file 7. Additional indel analysis. Data is presented from FreeBayes for a set of 5 selected indels identified by both FreeBayes and SNVer for coincidence cloning reads as compared to the B. melitensis 16M reference genome. For each of the samples indicated (provided as examples), the following are displayed: the total reads at the indel location from the RNA-sequencing sample, as mapped to the B. melitensis genome; the number of reads carrying the alternative (indel) allele; and the percent of mapped reads exhibiting the indel. &gt;â 92% of reads in each displayed location carried the indel of interest.
DOI: 10.7910/dvn/debtui/yp3awr
title: 0V

description: sigma=0volts
DOI: 10.6084/m9.figshare.6891518.v1
title: MOESM7 of Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis

description: Additional file 7. Additional indel analysis. Data is presented from FreeBayes for a set of 5 selected indels identified by both FreeBayes and SNVer for coincidence cloning reads as compared to the B. melitensis 16M reference genome. For each of the samples indicated (provided as examples), the following are displayed: the total reads at the indel location from the RNA-sequencing sample, as mapped to the B. melitensis genome; the number of reads carrying the alternative (indel) allele; and the percent of mapped reads exhibiting the indel. &gt;â 92% of reads in each displayed location carried the indel of interest.
DOI: 10.7910/dvn/debtui/evsepk
title: 0V

description: sigma=0volts
DOI: 10.6084/m9.figshare.6891509
title: Additional file 6: of A map of gene expression in neutrophil-like cell lines

description: Full tables of reanalyzed gene expression data for primary neutrophils and HL-60 cells from previously published studies. This Excel file contains four sheets. The first sheet contains FPKM gene expression values generated by Cufflinks for all primary human neutrophil and HL-60 samples reanalyzed in this study. The second sheet contains the corresponding log10-transformed normalized expression values. The third sheet contains FPKM gene expression values for all primary mouse neutrophil samples reanalyzed in this study, and the fourth sheet contains the corresponding log10-transformed normalized values. (XLSX 21707 kb)
DOI: 10.7910/dvn/debtui/dwoirw
title: 0V

description: sigma=0volts
DOI: 10.6084/m9.figshare.6891509.v1
title: Additional file 6: of A map of gene expression in neutrophil-like cell lines

description: Full tables of reanalyzed gene expression data for primary neutrophils and HL-60 cells from previously published studies. This Excel file contains four sheets. The first sheet contains FPKM gene expression values generated by Cufflinks for all primary human neutrophil and HL-60 samples reanalyzed in this study. The second sheet contains the corresponding log10-transformed normalized expression values. The third sheet contains FPKM gene expression values for all primary mouse neutrophil samples reanalyzed in this study, and the fourth sheet contains the corresponding log10-transformed normalized values. (XLSX 21707 kb)
DOI: 10.6084/m9.figshare.6891503
title: MOESM6 of Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis

description: Additional file 6. Indel analysis table across coincidence cloning samples. This table of indels present in the coincidence cloning reads was generated by SNVer analysis, as described in Methods, with only indels passing the read depth and significance filters displayed here. Columns A and B indicate the reference location of each indel on the chromosome (either I, indicated by NC_003317.1, or II, indicated by NC_003318.1). A “0” indicates the absence of the indel as compared to the B. melitensis 16M reference genome (matching the reference sequence) and a “1” indicates the presence of the indel. “Cultures 1–5” are B. melitensis broth culture-derived coincidence cloning samples, and the remaining samples are listed by their goat number. Rows in which all samples carried the designated indel are colored in green, and rows in which all but one of the samples carried the designated indel are colored in yellow. Please note that in cases where some samples did not exhibit the indel, this can be due to a read depth below the cutoff of &gt; 50 at the indel location for that sample, as used for the SNVer filter.
DOI: 10.7910/dvn/debtui/ckokcp
title: 0V

description: sigma=0volts
DOI: 10.6084/m9.figshare.6891503.v1
title: MOESM6 of Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis

description: Additional file 6. Indel analysis table across coincidence cloning samples. This table of indels present in the coincidence cloning reads was generated by SNVer analysis, as described in Methods, with only indels passing the read depth and significance filters displayed here. Columns A and B indicate the reference location of each indel on the chromosome (either I, indicated by NC_003317.1, or II, indicated by NC_003318.1). A “0” indicates the absence of the indel as compared to the B. melitensis 16M reference genome (matching the reference sequence) and a “1” indicates the presence of the indel. “Cultures 1–5” are B. melitensis broth culture-derived coincidence cloning samples, and the remaining samples are listed by their goat number. Rows in which all samples carried the designated indel are colored in green, and rows in which all but one of the samples carried the designated indel are colored in yellow. Please note that in cases where some samples did not exhibit the indel, this can be due to a read depth below the cutoff of &gt; 50 at the indel location for that sample, as used for the SNVer filter.
DOI: 10.7910/dvn/debtui/pgecbe
title: 0V

description: sigma=0volts
DOI: 10.7910/dvn/debtui/ejrou9
title: 0V

description: sigma=0volts
DOI: 10.7910/dvn/debtui/lauzke
title: 0V

description: sigma=0volts
DOI: 10.7910/dvn/debtui/egeiwy
title: 0V

description: sigma=0volts
DOI: 10.6084/m9.figshare.6891488
title: MOESM5 of Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis

description: Additional file 5. Sorted gene expression tables of top 100 genes by relative expression. Average gene length-normalized expression values (FPKM, calculated by SeqMonk) for the short-term and long-term coincidence cloning samples, generated as described in Additional file 4, were sorted by expression level for the short-term (left-hand columns) or the long-term (right-hand columns) samples. COG (Cluster of Orthologous Group) designations, as determined via the PHIDIAS Brucella Bioinformatics Portal ( www.phidias.us/bbp/ ), are annotated. The top 100 genes from each group in expression levels are provided. We note that there are challenges with the use of read data in FPKM/RPKM averaged across multiple samples, as discussed by Wagner et al. [67]. However, as depicted in Additional file 4, average FPKM values for each sample were very similar between biological replicates. We also completed an analysis in which the rank orders of gene expression were determined for each individual sample, and then genes were sorted by the lowest average rank order of expression.Â 96% of the long-term top 100 genes and 90% of the short-term top 100 genes were identical between the two methods. COG category single letter associations: amino acid transport and metabolism (E), carbohydrate transport and metabolism (G), cell cycle control and cell division, chromosome partitioning (D), cell motility (N), cell wall/membrane/envelope biogenesis (M), chromatin structure and dynamics (B), coenzyme transport and metabolism (H), cytoskeleton (Z), defense mechanisms (V), energy production and conversion (C), extracellular structures (W), function unknown (S), general function and prediction only (R), inorganic ion transport and metabolism (P), intracellular trafficking, secretion and vesicular transport (U), lipid transport and metabolism (I), nucleotide transport and metabolism (F), post-translational modification, protein turnover, chaperones (O), RNA processing and modification (A), replication, recombination and repair (L), secondary metabolites biosynthesis, transport and catabolism (Q), signal transduction mechanisms (T), transcription (K), translation, ribosomal structure and biogenesis (J).
DOI: 10.6084/m9.figshare.6891488.v1
title: MOESM5 of Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis

description: Additional file 5. Sorted gene expression tables of top 100 genes by relative expression. Average gene length-normalized expression values (FPKM, calculated by SeqMonk) for the short-term and long-term coincidence cloning samples, generated as described in Additional file 4, were sorted by expression level for the short-term (left-hand columns) or the long-term (right-hand columns) samples. COG (Cluster of Orthologous Group) designations, as determined via the PHIDIAS Brucella Bioinformatics Portal ( www.phidias.us/bbp/ ), are annotated. The top 100 genes from each group in expression levels are provided. We note that there are challenges with the use of read data in FPKM/RPKM averaged across multiple samples, as discussed by Wagner et al. [67]. However, as depicted in Additional file 4, average FPKM values for each sample were very similar between biological replicates. We also completed an analysis in which the rank orders of gene expression were determined for each individual sample, and then genes were sorted by the lowest average rank order of expression.Â 96% of the long-term top 100 genes and 90% of the short-term top 100 genes were identical between the two methods. COG category single letter associations: amino acid transport and metabolism (E), carbohydrate transport and metabolism (G), cell cycle control and cell division, chromosome partitioning (D), cell motility (N), cell wall/membrane/envelope biogenesis (M), chromatin structure and dynamics (B), coenzyme transport and metabolism (H), cytoskeleton (Z), defense mechanisms (V), energy production and conversion (C), extracellular structures (W), function unknown (S), general function and prediction only (R), inorganic ion transport and metabolism (P), intracellular trafficking, secretion and vesicular transport (U), lipid transport and metabolism (I), nucleotide transport and metabolism (F), post-translational modification, protein turnover, chaperones (O), RNA processing and modification (A), replication, recombination and repair (L), secondary metabolites biosynthesis, transport and catabolism (Q), signal transduction mechanisms (T), transcription (K), translation, ribosomal structure and biogenesis (J).
DOI: 10.7910/dvn/debtui/u7cv7v
title: 0-2.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/njoyez
title: 0-13.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6891482
title: Additional file 5: of A map of gene expression in neutrophil-like cell lines

description: Full tables of processed gene expression values measured by RNA-Seq in this study. This Excel file contains two sheets. The first sheet contains FPKM gene expression values generated by Cufflinks for all samples analyzed by RNA-Seq in this study. The second sheet contains the log10-transformed normalized expression values. These values were computed from the FPKM values as described in the Methods section. (XLSX 15648 kb)
DOI: 10.7910/dvn/debtui/dmnetr
title: 0-4.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6891482.v1
title: Additional file 5: of A map of gene expression in neutrophil-like cell lines

description: Full tables of processed gene expression values measured by RNA-Seq in this study. This Excel file contains two sheets. The first sheet contains FPKM gene expression values generated by Cufflinks for all samples analyzed by RNA-Seq in this study. The second sheet contains the log10-transformed normalized expression values. These values were computed from the FPKM values as described in the Methods section. (XLSX 15648 kb)
DOI: 10.7910/dvn/debtui/uzixri
title: 0-27.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6891473
title: MOESM7 of Spermatid-specific linker histone HILS1 is a poor condenser of DNA and chromatin and preferentially associates with LINE-1 elements

description: Additional file 7: Table S6. Repeat elements identification. Table represents the number of different types of repeat elements associated with HILS1.
DOI: 10.7910/dvn/debtui/xsayx1
title: 0-14.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6891473.v1
title: MOESM7 of Spermatid-specific linker histone HILS1 is a poor condenser of DNA and chromatin and preferentially associates with LINE-1 elements

description: Additional file 7: Table S6. Repeat elements identification. Table represents the number of different types of repeat elements associated with HILS1.
DOI: 10.7910/dvn/debtui/rmhmbe
title: 0-21.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6891467
title: MOESM4 of Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis

description: Additional file 4. Gene expression values for short- and long-term goat samples. Annotated probe table prepared for coincidence cloning samples for goats 1â 3 (short-term) and goats 4â 7 (long-term) using SeqMonk. Libraries were treated as paired-end upon loading into SeqMonk. Quantitation was performed using the RNA-Sequencing pipeline in SeqMonk, using the option for normalization of values to gene size (per kilobase of transcript per million mapped reads, or FPKM, based on SeqMonk documentation), and expression values are expressed as log2 transformations of FPKM values. Start and end columns indicate locations of each quantitated feature in the B. melitensis 16M reference genome.
DOI: 10.6084/m9.figshare.6891467.v1
title: MOESM4 of Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis

description: Additional file 4. Gene expression values for short- and long-term goat samples. Annotated probe table prepared for coincidence cloning samples for goats 1â 3 (short-term) and goats 4â 7 (long-term) using SeqMonk. Libraries were treated as paired-end upon loading into SeqMonk. Quantitation was performed using the RNA-Sequencing pipeline in SeqMonk, using the option for normalization of values to gene size (per kilobase of transcript per million mapped reads, or FPKM, based on SeqMonk documentation), and expression values are expressed as log2 transformations of FPKM values. Start and end columns indicate locations of each quantitated feature in the B. melitensis 16M reference genome.
DOI: 10.7910/dvn/debtui/dhjyrd
title: 0-26.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/poy64w
title: 0-22.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6891458
title: MOESM6 of Spermatid-specific linker histone HILS1 is a poor condenser of DNA and chromatin and preferentially associates with LINE-1 elements

description: Additional file 6: Table S5. Annotation of the overlapping peaks using HOMER. Overlapping peaks were re-annotated using HOMERv4.7 with newly defined overlap peak lengths and table represents the chromosome-wise number of peaks associated with specific genomic regions like intergenic, intron, exon, 3â ˛UTR, TTS, and promoter-TSS.
DOI: 10.7910/dvn/debtui/3r1yar
title: 0-42.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6891458.v1
title: MOESM6 of Spermatid-specific linker histone HILS1 is a poor condenser of DNA and chromatin and preferentially associates with LINE-1 elements

description: Additional file 6: Table S5. Annotation of the overlapping peaks using HOMER. Overlapping peaks were re-annotated using HOMERv4.7 with newly defined overlap peak lengths and table represents the chromosome-wise number of peaks associated with specific genomic regions like intergenic, intron, exon, 3â ˛UTR, TTS, and promoter-TSS.
DOI: 10.7910/dvn/debtui/w26zx6
title: 0-29.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/xdwkgo
title: 0-31.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/pmkkbb
title: 0-34.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/endsif
title: 0-1.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6891440
title: MOESM5 of Spermatid-specific linker histone HILS1 is a poor condenser of DNA and chromatin and preferentially associates with LINE-1 elements

description: Additional file 5: Table S4. ChIP peaks (32731) overlapping with UCSC CpG islands. List of CpG islands were obtained from UCSC table browser and used to find overlaps with 32731 HILS1 ChIP peaks using Bed tools Intersect.
DOI: 10.6084/m9.figshare.6891443
title: Additional file 3: of Chronic Toxoplasma infection is associated with distinct alterations in the synaptic protein composition

description: Proteomic analysis of synaptosomes from T. gondii infected mice. Compilation of 292 significantly regulated proteins found at minimum in three biological replicates. (XLS 1760Â kb)
DOI: 10.7910/dvn/debtui/mephfe
title: 0-25.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6891440.v1
title: MOESM5 of Spermatid-specific linker histone HILS1 is a poor condenser of DNA and chromatin and preferentially associates with LINE-1 elements

description: Additional file 5: Table S4. ChIP peaks (32731) overlapping with UCSC CpG islands. List of CpG islands were obtained from UCSC table browser and used to find overlaps with 32731 HILS1 ChIP peaks using Bed tools Intersect.
DOI: 10.6084/m9.figshare.6891443.v1
title: Additional file 3: of Chronic Toxoplasma infection is associated with distinct alterations in the synaptic protein composition

description: Proteomic analysis of synaptosomes from T. gondii infected mice. Compilation of 292 significantly regulated proteins found at minimum in three biological replicates. (XLS 1760Â kb)
DOI: 10.7910/dvn/debtui/g33qix
title: 0-18.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/d0zoxj
title: 0-20.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/u2zeyq
title: 0-47.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/ubyhoa
title: 0-35.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/u5i5l1
title: 0-32.25V

description: sigma=0.25V; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6891425
title: MOESM4 of Spermatid-specific linker histone HILS1 is a poor condenser of DNA and chromatin and preferentially associates with LINE-1 elements

description: Additional file 4: Table S3. Chromosome-wise peak length of HILS1 peaks. Excel file represents the length of HILS1 peaks across the chromosomes confirming their broad nature
DOI: 10.6084/m9.figshare.6891425.v1
title: MOESM4 of Spermatid-specific linker histone HILS1 is a poor condenser of DNA and chromatin and preferentially associates with LINE-1 elements

description: Additional file 4: Table S3. Chromosome-wise peak length of HILS1 peaks. Excel file represents the length of HILS1 peaks across the chromosomes confirming their broad nature