cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3913765_d2
title: Additional file 2: Table S2 of Molecular investigation of Cryptosporidium and Giardia in pre- and post-weaned calves in Hubei Province, China

description: Summary of information on the reference sequences from the GenBank database used in the present study. (XLSX 55 kb)
DOI: 10.6084/m9.figshare.c.3913762_d1.v1
title: MOESM1 of Identification of differentially expressed genes in sunflower (Helianthus annuus) leaves and roots under drought stress by RNA sequencing

description: Additional file 1: Table S1. The sequences of primers of qRT-PCR.
DOI: 10.6084/m9.figshare.c.3913765_d1.v1
title: Additional file 1: Table S1 of Molecular investigation of Cryptosporidium and Giardia in pre- and post-weaned calves in Hubei Province, China

description: Oligonucleotide primers and PCR protocol used in this study. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.c.3913765_d1
title: Additional file 1: Table S1 of Molecular investigation of Cryptosporidium and Giardia in pre- and post-weaned calves in Hubei Province, China

description: Oligonucleotide primers and PCR protocol used in this study. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.c.3912787_d2
title: Additional file 2: Dataset_S1. of A heuristic model for computational prediction of human branch point sequence

description: (FASTA 146 kb)
DOI: 10.6084/m9.figshare.c.3911707_d8.v1
title: Additional file 7: of Comparative transcriptomic analyses of normal and malformed flowers in sugar apple (Annona squamosa L.) to identify the differential expressed genes between normal and malformed flowers

description: The gene list of GO:0009908. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3911707_d7.v1
title: Additional file 6: of Comparative transcriptomic analyses of normal and malformed flowers in sugar apple (Annona squamosa L.) to identify the differential expressed genes between normal and malformed flowers

description: Identification of key flowering- and flower development-related DEGs. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3911707_d8
title: Additional file 7: of Comparative transcriptomic analyses of normal and malformed flowers in sugar apple (Annona squamosa L.) to identify the differential expressed genes between normal and malformed flowers

description: The gene list of GO:0009908. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3911707_d7
title: Additional file 6: of Comparative transcriptomic analyses of normal and malformed flowers in sugar apple (Annona squamosa L.) to identify the differential expressed genes between normal and malformed flowers

description: Identification of key flowering- and flower development-related DEGs. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3911707_d6.v1
title: Additional file 5: of Comparative transcriptomic analyses of normal and malformed flowers in sugar apple (Annona squamosa L.) to identify the differential expressed genes between normal and malformed flowers

description: The information of 21 MADS-box genes were revealed from sugar apple flowers. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3911707_d5.v1
title: Additional file 4: of Comparative transcriptomic analyses of normal and malformed flowers in sugar apple (Annona squamosa L.) to identify the differential expressed genes between normal and malformed flowers

description: The information of 701 TF genes were identified as DEGs. (XLSX 21Â kb)
DOI: 10.6084/m9.figshare.c.3911707_d6
title: Additional file 5: of Comparative transcriptomic analyses of normal and malformed flowers in sugar apple (Annona squamosa L.) to identify the differential expressed genes between normal and malformed flowers

description: The information of 21 MADS-box genes were revealed from sugar apple flowers. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3911707_d4
title: Additional file 3: of Comparative transcriptomic analyses of normal and malformed flowers in sugar apple (Annona squamosa L.) to identify the differential expressed genes between normal and malformed flowers

description: KEGG classifications of unigenes. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3911707_d5
title: Additional file 4: of Comparative transcriptomic analyses of normal and malformed flowers in sugar apple (Annona squamosa L.) to identify the differential expressed genes between normal and malformed flowers

description: The information of 701 TF genes were identified as DEGs. (XLSX 21Â kb)
DOI: 10.6084/m9.figshare.c.3911707_d4.v1
title: Additional file 3: of Comparative transcriptomic analyses of normal and malformed flowers in sugar apple (Annona squamosa L.) to identify the differential expressed genes between normal and malformed flowers

description: KEGG classifications of unigenes. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3911638_d2.v1
title: Additional file 2: of Systematic identification of regulatory variants associated with cancer risk

description: Supplementary datasets. (XLSX 2496Â kb)
DOI: 10.6084/m9.figshare.c.3911638_d2
title: Additional file 2: of Systematic identification of regulatory variants associated with cancer risk

description: Supplementary datasets. (XLSX 2496Â kb)
DOI: 10.6084/m9.figshare.c.3911617_d2
title: Additional file 2: of High-resolution manometry in patients with and without globus pharyngeus and/or symptoms of laryngopharyngeal reflux

description: Life exposure factors questionnaire. (ZIP 45 kb)
DOI: 10.6084/m9.figshare.c.3911617_d2.v1
title: Additional file 2: of High-resolution manometry in patients with and without globus pharyngeus and/or symptoms of laryngopharyngeal reflux

description: Life exposure factors questionnaire. (ZIP 45 kb)
DOI: 10.6084/m9.figshare.c.3911605_d2.v1
title: Additional file 2: Figure S1 and S2. of dCATCH-Seq: improved sequencing of large continuous genomic targets with double-hybridization

description: Visualization of reads mapping to three SNVs (S1) and two Indels (S2) called for dCATCH-Seq (left panel) and CATCH-Seq (right panel) methods. Red-colored arrows show the location of the discordantly called SNVs (S1) and Indels (S2). Figure S3. Visualization of reads mapping to two Indels (A and B) from an independent CATCH-Seq assay in two replicates. Red-colored arrows, the location of the confirmed Indels. Figure S4. SVs in K562 cells. The upper panels are SVs detected by conditions (with or without PCR) after the first capture. The lower panels are SVs identified by a previous study. Figure S5. Two novel deletions in K562 cells. PCR primer pairs for verifying a homozygous deletion (A) and a heterozygous deletion (C), and the agarose gel electrophoresis results (B and D). P, N and M denote the positive, negative bands and DNA marker, respectively. Due to difficulty in design of the specific primers, there is a second (non-specific) band for the N2 lane. Figure S6. Genome-wide read coverage in U937 cell genome using the dCATCH-Seq. Red bars represent the read depth in 5 kb windows. Black bars mean the gap (unassembled) regions in the reference human genome. Figure S7. Scatterplot showing read counts (log2-transformed) on two alleles for heterozygous variants across the MHC region in U937 cell genome. Colors in a rainbow mode represent the density of heterozygous variants. Figure S8. Comparison of DNA methylation levels at a region on chr11 (A-B) and on the MHC region (C-D) calculated by read counts with (x-axis) or without (y-axis) removal of PCR duplicates in a CpG (left panel) or non-CpG (right panel) dinucleotide context. Histograms (A and C) represent the distribution of CpG methylation levels corresponding to x- and y-axes, respectively. (ZIP 8432 kb)
DOI: 10.6084/m9.figshare.c.3911605_d2
title: Additional file 2: Figure S1 and S2. of dCATCH-Seq: improved sequencing of large continuous genomic targets with double-hybridization

description: Visualization of reads mapping to three SNVs (S1) and two Indels (S2) called for dCATCH-Seq (left panel) and CATCH-Seq (right panel) methods. Red-colored arrows show the location of the discordantly called SNVs (S1) and Indels (S2). Figure S3. Visualization of reads mapping to two Indels (A and B) from an independent CATCH-Seq assay in two replicates. Red-colored arrows, the location of the confirmed Indels. Figure S4. SVs in K562 cells. The upper panels are SVs detected by conditions (with or without PCR) after the first capture. The lower panels are SVs identified by a previous study. Figure S5. Two novel deletions in K562 cells. PCR primer pairs for verifying a homozygous deletion (A) and a heterozygous deletion (C), and the agarose gel electrophoresis results (B and D). P, N and M denote the positive, negative bands and DNA marker, respectively. Due to difficulty in design of the specific primers, there is a second (non-specific) band for the N2 lane. Figure S6. Genome-wide read coverage in U937 cell genome using the dCATCH-Seq. Red bars represent the read depth in 5 kb windows. Black bars mean the gap (unassembled) regions in the reference human genome. Figure S7. Scatterplot showing read counts (log2-transformed) on two alleles for heterozygous variants across the MHC region in U937 cell genome. Colors in a rainbow mode represent the density of heterozygous variants. Figure S8. Comparison of DNA methylation levels at a region on chr11 (A-B) and on the MHC region (C-D) calculated by read counts with (x-axis) or without (y-axis) removal of PCR duplicates in a CpG (left panel) or non-CpG (right panel) dinucleotide context. Histograms (A and C) represent the distribution of CpG methylation levels corresponding to x- and y-axes, respectively. (ZIP 8432 kb)
DOI: 10.6084/m9.figshare.c.3911389_d9
title: Additional file 9: Table S2. of Preliminary comparative genomics revealed pathogenic potential and international spread of Staphylococcus argenteus

description: Prevalence and relatedness of virulence genes among S. aureus complex (SAC) genomes. The presence/absence and interspecies divergence was analyzed for 111 virulence genes from 51 SAC genomes (30 S. aureus, 15 S. argenteus and 6 S. schweitzeri. Five virulence genes, sed, see, sej, selr and etb, are not listed in the table because they were not detected in any of the 51 SAC genomes examined. a *, these genes have tandem repeat regions, so the interspecies divergence of the nucleotide sequences may not clearly reflect the true evolutionary divergence. b The number of SAC genomes of each species harboring each virulence gene. c The gene family numbers as listed in Additional file 3: Table S1. d NA, not applicable; SA, S. aureus; SG, S. argenteus; SW, S. schweitzeri. e Maximum likelihood phylogenetic trees were contructed based on nucleotide sequence, using substitution matrix GTR and executing 100 rapid bootstrap inferences. The species names were omitted in tip labels. f p.g., pseudogene. (XLSX 1797 kb)
DOI: 10.6084/m9.figshare.c.3911389_d9.v1
title: Additional file 9: Table S2. of Preliminary comparative genomics revealed pathogenic potential and international spread of Staphylococcus argenteus

description: Prevalence and relatedness of virulence genes among S. aureus complex (SAC) genomes. The presence/absence and interspecies divergence was analyzed for 111 virulence genes from 51 SAC genomes (30 S. aureus, 15 S. argenteus and 6 S. schweitzeri. Five virulence genes, sed, see, sej, selr and etb, are not listed in the table because they were not detected in any of the 51 SAC genomes examined. a *, these genes have tandem repeat regions, so the interspecies divergence of the nucleotide sequences may not clearly reflect the true evolutionary divergence. b The number of SAC genomes of each species harboring each virulence gene. c The gene family numbers as listed in Additional file 3: Table S1. d NA, not applicable; SA, S. aureus; SG, S. argenteus; SW, S. schweitzeri. e Maximum likelihood phylogenetic trees were contructed based on nucleotide sequence, using substitution matrix GTR and executing 100 rapid bootstrap inferences. The species names were omitted in tip labels. f p.g., pseudogene. (XLSX 1797 kb)
DOI: 10.6084/m9.figshare.c.3911380_d9
title: Additional file 8: of Unsupervised gene expression analyses identify IPF-severity correlated signatures, associated genes and biomarkers

description: Table S3. List of genes used as training set for ToppGene prioritization. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.c.3911380_d9.v1
title: Additional file 8: of Unsupervised gene expression analyses identify IPF-severity correlated signatures, associated genes and biomarkers

description: Table S3. List of genes used as training set for ToppGene prioritization. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.c.3909649_d23.v1
title: Additional file 8: Table S7. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Unigenes differentially expressed between black and brown dry seed. (XLSX 270 kb)
DOI: 10.6084/m9.figshare.c.3909649_d24.v1
title: Additional file 9: Table S8. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Annotation of unigenes differentially expressed between black and brown dry seed compared with KEGG database. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.c.3909649_d23
title: Additional file 8: Table S7. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Unigenes differentially expressed between black and brown dry seed. (XLSX 270 kb)
DOI: 10.6084/m9.figshare.c.3909649_d22.v1
title: Additional file 7: Table S6. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Annotation of unigenes differentially expressed during Suaeda aralocaspica seed germination compared with KEGG database. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.c.3909649_d21.v1
title: Additional file 6: Table S5. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Unigenes differentially expressed during Suaeda aralocaspica seed germination. (XLSX 3688 kb)
DOI: 10.6084/m9.figshare.c.3909649_d22
title: Additional file 7: Table S6. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Annotation of unigenes differentially expressed during Suaeda aralocaspica seed germination compared with KEGG database. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.c.3909649_d21
title: Additional file 6: Table S5. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Unigenes differentially expressed during Suaeda aralocaspica seed germination. (XLSX 3688 kb)
DOI: 10.6084/m9.figshare.c.3909649_d20.v1
title: Additional file 5: Table S4. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Unigene RPKM value and annotation against Nr database at NCBI. (XLSX 5600 kb)
DOI: 10.6084/m9.figshare.c.3909649_d20
title: Additional file 5: Table S4. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Unigene RPKM value and annotation against Nr database at NCBI. (XLSX 5600 kb)
DOI: 10.6084/m9.figshare.c.3909649_d16.v1
title: Additional file 24: Table S21. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: The primers used in this study. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3909649_d16
title: Additional file 24: Table S21. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: The primers used in this study. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3909649_d14.v1
title: Additional file 22: Table S19. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Unigenes involved in photosynthesis-antenna proteins pathway identified by KEGG enrichment. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3909649_d15.v1
title: Additional file 23: Table S20. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Unigenes involved in photosynthesis pathway identified by KEGG enrichment. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.c.3909649_d15
title: Additional file 23: Table S20. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Unigenes involved in photosynthesis pathway identified by KEGG enrichment. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.c.3909649_d14
title: Additional file 22: Table S19. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Unigenes involved in photosynthesis-antenna proteins pathway identified by KEGG enrichment. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3909649_d12.v1
title: Additional file 20: Table S18. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Expression profiles of unigenes/miRNAs measured by RNA/small RNA sequencing and real-time qRT-PCR. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.c.3909649_d12
title: Additional file 20: Table S18. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Expression profiles of unigenes/miRNAs measured by RNA/small RNA sequencing and real-time qRT-PCR. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.c.3909649_d3
title: Additional file 12: Table S12. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Identification of conserved miRNAs in Suaeda aralocaspica. (XLSX 76 kb)
DOI: 10.6084/m9.figshare.c.3909649_d2.v1
title: Additional file 11: Table S10. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Identification of differentially expressed unigenes involved in circadian rhythm-plant pathway during black seed germination. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3909649_d2
title: Additional file 11: Table S10. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Identification of differentially expressed unigenes involved in circadian rhythm-plant pathway during black seed germination. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3909649_d1
title: Additional file 10: Table S9. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Identification of unigenes involved in abscisic acid and gibberellic acid signal transduction. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3909649_d1.v1
title: Additional file 10: Table S9. of Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

description: Identification of unigenes involved in abscisic acid and gibberellic acid signal transduction. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3908473_d12
title: Additional file 9: Table S6. of The dynamics of smoking-related disturbed methylation: a two time-point study of methylation change in smokers, non-smokers and former smokers

description: Spearman correlations between longitudinal coefficients and cross-sectional coefficients for each time since quitting smoking category. The longitudinal coefficients represent the rate of change of methylation M-value per year between baseline and follow-up relative to never smokers. The cross-sectional coefficients represent the methylation difference to never smokers at baseline. The correlations and p-values are given when using only the sites that are longitudinally significant for that smoking category, when using sites that are longitudinally significant for any smoking category, and when using all 590 investigated sites. (XLS 33 kb)
DOI: 10.6084/m9.figshare.c.3908473_d12.v1
title: Additional file 9: Table S6. of The dynamics of smoking-related disturbed methylation: a two time-point study of methylation change in smokers, non-smokers and former smokers

description: Spearman correlations between longitudinal coefficients and cross-sectional coefficients for each time since quitting smoking category. The longitudinal coefficients represent the rate of change of methylation M-value per year between baseline and follow-up relative to never smokers. The cross-sectional coefficients represent the methylation difference to never smokers at baseline. The correlations and p-values are given when using only the sites that are longitudinally significant for that smoking category, when using sites that are longitudinally significant for any smoking category, and when using all 590 investigated sites. (XLS 33 kb)
DOI: 10.6084/m9.figshare.c.3908473_d9.v1
title: Additional file 6: Table S5. of The dynamics of smoking-related disturbed methylation: a two time-point study of methylation change in smokers, non-smokers and former smokers

description: Gene overrepresentation analysis results based on the WebGestalt platform ( webgestalt.org ). For each TSQL category we extracted the CpG sites that showed nominal significance (p
DOI: 10.6084/m9.figshare.c.3908473_d9
title: Additional file 6: Table S5. of The dynamics of smoking-related disturbed methylation: a two time-point study of methylation change in smokers, non-smokers and former smokers

description: Gene overrepresentation analysis results based on the WebGestalt platform ( webgestalt.org ). For each TSQL category we extracted the CpG sites that showed nominal significance (p
DOI: 10.15468/dl.es2cnv
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Guinea, Congo, Sierra Leone, Côte d’Ivoire)",
 {
 "or" : [
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "Geometry POLYGON((67.22893 -18.07276,65.75424 3.3696,44.37124 39.44844,-3.55617 44.25746,-141.43965 11.86676,-82.02108 -65.16361,74.60238 -39.41175,67.22893 -18.07276))"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rubricatochromis Lamboj & Koblmüller, 2022"
 ]
}

 The dataset includes 20 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035398-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3908473_d1.v1
title: Additional file 10: Table S7. of The dynamics of smoking-related disturbed methylation: a two time-point study of methylation change in smokers, non-smokers and former smokers

description: All results of the analysis of longitudinal effect of continued smoking. The longitudinal regression coefficients represent the rate of change of methylation M-value per year from baseline to follow-up for continued smokers relative to never smokers. The cross-sectional coefficients represent the methylation M-value difference to never smokers at baseline. Also presented are the results for the time coefficient from the model. “Chromosome” is the chromosome of the CpG site and “Gene or region” is based on the annotation file provided by Illumina (HumanMethylation450 v1.2 Manifest File). (XLS 179 kb)