cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12586634
title: Additional file 3 of Prognostic imaging biomarkers for diabetic kidney disease (iBEAt): study protocol

description: Additional file 3: 3.0 CRF Screening. PDF file. Study recruitment – prescreening / screening. Clinical record form for prescreening / screening data. 3.1 CRF Adherence Checklist. PDF file. Baseline visit (V1) – adherence checklist. Clinical record form documenting participant adherence to guidance for the baseline visit. 3.2 CRF Limited Clinical Exam. PDF file. Limited Clinical Exam. Clinical record form for clinical examination data including, for example, blood pressure, height and weight. 3.3 CRF Medical and Family Hx. PDF file. Baseline (V1) – Medical and family history V2. Clinical record form for medical and family history (version 2). 3.4 CRF Local Study Labs. PDF file. Baseline (V1) – local study labs. Clinical record form for laboratory measurements performed at recruiting centre. 3.5 CRF Routine Labs. PDF file. Baseline visit (V1) – labs. Clinical record form for documenting all available laboratory values in the year prior to the baseline visit. 3.6 CRF Medications. PDF file. Medication log. Clinical record form documenting all current medications. 3.7 CRF Ultrasound. PDF file. Baseline visit (V1) – Ultrasound. Clinical record form for the renal ultrasound measurements. 3.8 CRF Biosamples. PDF file. Study biosamples. Clinical record form / checklist documenting what biofluid samples were collected and processed for the iBEAt study.
DOI: 10.6084/m9.figshare.12586636
title: Additional file 3 of Effect of phyB and phyC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods

description: Additional file 3. RNA-seq data for all samples from LD photoperiods.
DOI: 10.6084/m9.figshare.12586637.v1
title: Additional file 4 of Prognostic imaging biomarkers for diabetic kidney disease (iBEAt): study protocol

description: Additional file 4: 4.0 Biopsy SOP. PDF file. Biopsy and pathology SOPs. Protocol for storing and capturing meta-data regarding the renal biopsy tissue for the iBEAt study. (EXE 543 kb)
DOI: 10.6084/m9.figshare.12586639.v1
title: Additional file 4 of Effect of phyB and phyC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods

description: Additional file 4 RNA-seq data and annotations of genes regulated by PHYB or PHYC under SD or LD, divided into mutually exclusive categories.
DOI: 10.6084/m9.figshare.12586634.v1
title: Additional file 3 of Prognostic imaging biomarkers for diabetic kidney disease (iBEAt): study protocol

description: Additional file 3: 3.0 CRF Screening. PDF file. Study recruitment – prescreening / screening. Clinical record form for prescreening / screening data. 3.1 CRF Adherence Checklist. PDF file. Baseline visit (V1) – adherence checklist. Clinical record form documenting participant adherence to guidance for the baseline visit. 3.2 CRF Limited Clinical Exam. PDF file. Limited Clinical Exam. Clinical record form for clinical examination data including, for example, blood pressure, height and weight. 3.3 CRF Medical and Family Hx. PDF file. Baseline (V1) – Medical and family history V2. Clinical record form for medical and family history (version 2). 3.4 CRF Local Study Labs. PDF file. Baseline (V1) – local study labs. Clinical record form for laboratory measurements performed at recruiting centre. 3.5 CRF Routine Labs. PDF file. Baseline visit (V1) – labs. Clinical record form for documenting all available laboratory values in the year prior to the baseline visit. 3.6 CRF Medications. PDF file. Medication log. Clinical record form documenting all current medications. 3.7 CRF Ultrasound. PDF file. Baseline visit (V1) – Ultrasound. Clinical record form for the renal ultrasound measurements. 3.8 CRF Biosamples. PDF file. Study biosamples. Clinical record form / checklist documenting what biofluid samples were collected and processed for the iBEAt study.
DOI: 10.6084/m9.figshare.12586636.v1
title: Additional file 3 of Effect of phyB and phyC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods

description: Additional file 3. RNA-seq data for all samples from LD photoperiods.
DOI: 10.6084/m9.figshare.12586625
title: Additional file 1 of Prognostic imaging biomarkers for diabetic kidney disease (iBEAt): study protocol

description: Additional file 1: 1.1 MRI biomarkers. File type: PDF file. Title: List of primary MRI biomarkers. Description: A table listing the biomarkers that will be derived from the MRI data to address the primary objectives. 1.2 MRI acquisition protocol. PDF file. MRI acquisition protocol (reference scanner). MRI sequence parameters for the iBEAt protocol on the reference scanner (Siemens 3 T). 1.3 Renal ultrasound SOP. PDF file. Ultrasound Standard Operating Procedures. Standard operating procedures for Ultrasound scanning in iBEAt.
DOI: 10.6084/m9.figshare.12586628
title: Additional file 2 of Prognostic imaging biomarkers for diabetic kidney disease (iBEAt): study protocol

description: Additional file 2: 2.1 Biofluid collection SOPs. PDF file. Biofluid collection protocol. The protocol for the collection of blood and urine samples within iBEAt. 2.2 SOPs Biofluid processing. PDF file. Biofluid processing protocol. The protocol for processing blood and urine samples within iBEAt. 2.3 Biofluid schematics. PDF file. iBEAt kit contents and biofluid processing schematics. Schematics of iBEAt collection kits, and processing and storage protocols for collected blood and urine samples within iBEAt.
DOI: 10.6084/m9.figshare.12586633.v1
title: Additional file 2 of Effect of phyB and phyC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods

description: Additional file 2. RNA-seq data for all samples from SD photoperiods.
DOI: 10.6084/m9.figshare.12586625.v1
title: Additional file 1 of Prognostic imaging biomarkers for diabetic kidney disease (iBEAt): study protocol

description: Additional file 1: 1.1 MRI biomarkers. File type: PDF file. Title: List of primary MRI biomarkers. Description: A table listing the biomarkers that will be derived from the MRI data to address the primary objectives. 1.2 MRI acquisition protocol. PDF file. MRI acquisition protocol (reference scanner). MRI sequence parameters for the iBEAt protocol on the reference scanner (Siemens 3 T). 1.3 Renal ultrasound SOP. PDF file. Ultrasound Standard Operating Procedures. Standard operating procedures for Ultrasound scanning in iBEAt.
DOI: 10.6084/m9.figshare.12586628.v1
title: Additional file 2 of Prognostic imaging biomarkers for diabetic kidney disease (iBEAt): study protocol

description: Additional file 2: 2.1 Biofluid collection SOPs. PDF file. Biofluid collection protocol. The protocol for the collection of blood and urine samples within iBEAt. 2.2 SOPs Biofluid processing. PDF file. Biofluid processing protocol. The protocol for processing blood and urine samples within iBEAt. 2.3 Biofluid schematics. PDF file. iBEAt kit contents and biofluid processing schematics. Schematics of iBEAt collection kits, and processing and storage protocols for collected blood and urine samples within iBEAt.
DOI: 10.6084/m9.figshare.12586613
title: Additional file 1 of Biofilm formation, antimicrobial susceptibility and virulence genes of Uropathogenic Escherichia coli isolated from clinical isolates in Uganda

description: Additional file 1.
DOI: 10.6084/m9.figshare.12586613.v1
title: Additional file 1 of Biofilm formation, antimicrobial susceptibility and virulence genes of Uropathogenic Escherichia coli isolated from clinical isolates in Uganda

description: Additional file 1.
DOI: 10.6084/m9.figshare.12586556
title: Additional file 7 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 7. The data file that can be accessed using free software GEPHI available at https://gephi.org/ comprising of Data S1: Gene regulatory network in cold acclimation, Data S2: Cold responsive network of the differentially expressed miRNAs.
DOI: 10.6084/m9.figshare.12586547
title: Additional file 4 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 4 Table S9: List of all mRNAs generated from mRNA sequencing data. The three sub-tables depict normalized read counts (triplicates) from control and cold treated samples at 3 h, 6 h and 2 d. Table S10: List of all significant DE mRNAs generated from mRNA sequencing data. The sub-tables present all the details from control and cold treated samples after 3 h, 6 h and 2 d.
DOI: 10.6084/m9.figshare.12586550
title: Additional file 5 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 5 Table S11: List of 54 targets of differentially expressed miRNAs from all the four subgroups found to be consistently present at all the three time points. The Venn diagram depicts all targets of differentially expressed miRNAs observed after 3 h, 6 h and 2 d.
DOI: 10.6084/m9.figshare.12586553
title: Additional file 6 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 6 Table S12: Gene Ontology term enrichment analysis for predicted targets of differentially expressed miRNAs. The sub-tables depict GO terms after 3 h, 6 h and 2 d of cold acclimation.
DOI: 10.6084/m9.figshare.12586550.v1
title: Additional file 5 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 5 Table S11: List of 54 targets of differentially expressed miRNAs from all the four subgroups found to be consistently present at all the three time points. The Venn diagram depicts all targets of differentially expressed miRNAs observed after 3 h, 6 h and 2 d.
DOI: 10.6084/m9.figshare.12586553.v1
title: Additional file 6 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 6 Table S12: Gene Ontology term enrichment analysis for predicted targets of differentially expressed miRNAs. The sub-tables depict GO terms after 3 h, 6 h and 2 d of cold acclimation.
DOI: 10.6084/m9.figshare.12586556.v1
title: Additional file 7 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 7. The data file that can be accessed using free software GEPHI available at https://gephi.org/ comprising of Data S1: Gene regulatory network in cold acclimation, Data S2: Cold responsive network of the differentially expressed miRNAs.
DOI: 10.6084/m9.figshare.12586535
title: Additional file 14 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 14 Table S18: Sequences of oligonucleotides used in this study to perform stem loop qRT-PCR.
DOI: 10.6084/m9.figshare.12586541
title: Additional file 2 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 2 Table S4: Differentially expressed miRNAs during cold acclimation. The three sub-tables depict DE miRNAs at 3 h, 6 h and 2 d, respectively. The miRNAs highlighted in orange belong to evolutionarily conserved miRNA families. Table S5: Normalized read counts and fold changes of all miRNAs during cold acclimation. The three sub-tables depict all miRNAs at 3 h, 6 h and 2 d, respectively. Table S6: Differentially expressed cold-responsive miRNAs in A. thaliana. Fold changes of miRNAs after 3 h, 6 h and 2 d of cold treatment, considered DE when log2FC ≥ 1& ≤ − 1, Benjamini-Hochberg corrected p-value ≤0.05, Conserved miRNAs are highlighted in bold.
DOI: 10.6084/m9.figshare.12586544
title: Additional file 3 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 3 Table S7: List of miRNA-targeted mRNAs predicted using psRNATarget. The sub-tables depict all predicted targets of DE miRNAs at the three time points. A stringent expectation value of 2.5 was used to filter the targets. N/A = No significant fold change Table S8: List of miRNA-targeted ncRNAs predicted using psRNATarget. The sub-tables depict all predicted ncRNA targets of DE miRNAs at the three time points. A stringent expectation value of 2.5 was used to filter the targets. N/A = No significant fold change .
DOI: 10.6084/m9.figshare.12586547.v1
title: Additional file 4 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 4 Table S9: List of all mRNAs generated from mRNA sequencing data. The three sub-tables depict normalized read counts (triplicates) from control and cold treated samples at 3 h, 6 h and 2 d. Table S10: List of all significant DE mRNAs generated from mRNA sequencing data. The sub-tables present all the details from control and cold treated samples after 3 h, 6 h and 2 d.
DOI: 10.6084/m9.figshare.12586535.v1
title: Additional file 14 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 14 Table S18: Sequences of oligonucleotides used in this study to perform stem loop qRT-PCR.
DOI: 10.6084/m9.figshare.12586538
title: Additional file 1 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 1 Table S1: Total mRNA sequencing reads mapping to the A. thaliana reference genome after adapter trimming in control and cold treated samples (biological triplicates). Table S2: Total sRNA sequencing reads mapping to different sRNA producing RNA classes for control and cold treated samples. Table S3: sRNA size distribution in reads per million. The size distribution of total sRNAs derived from control and cold treated samples after adapter trimming.
DOI: 10.6084/m9.figshare.12586541.v1
title: Additional file 2 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 2 Table S4: Differentially expressed miRNAs during cold acclimation. The three sub-tables depict DE miRNAs at 3 h, 6 h and 2 d, respectively. The miRNAs highlighted in orange belong to evolutionarily conserved miRNA families. Table S5: Normalized read counts and fold changes of all miRNAs during cold acclimation. The three sub-tables depict all miRNAs at 3 h, 6 h and 2 d, respectively. Table S6: Differentially expressed cold-responsive miRNAs in A. thaliana. Fold changes of miRNAs after 3 h, 6 h and 2 d of cold treatment, considered DE when log2FC ≥ 1& ≤ − 1, Benjamini-Hochberg corrected p-value ≤0.05, Conserved miRNAs are highlighted in bold.
DOI: 10.6084/m9.figshare.12586544.v1
title: Additional file 3 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 3 Table S7: List of miRNA-targeted mRNAs predicted using psRNATarget. The sub-tables depict all predicted targets of DE miRNAs at the three time points. A stringent expectation value of 2.5 was used to filter the targets. N/A = No significant fold change Table S8: List of miRNA-targeted ncRNAs predicted using psRNATarget. The sub-tables depict all predicted ncRNA targets of DE miRNAs at the three time points. A stringent expectation value of 2.5 was used to filter the targets. N/A = No significant fold change .
DOI: 10.6084/m9.figshare.12586532
title: Additional file 13 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 13 Table S17: List of classical cold responsive genes that were found to be differentially expressed in Lee et al. 2005 and are also differential expression in our study.
DOI: 10.6084/m9.figshare.12586532.v1
title: Additional file 13 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 13 Table S17: List of classical cold responsive genes that were found to be differentially expressed in Lee et al. 2005 and are also differential expression in our study.
DOI: 10.6084/m9.figshare.12586538.v1
title: Additional file 1 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 1 Table S1: Total mRNA sequencing reads mapping to the A. thaliana reference genome after adapter trimming in control and cold treated samples (biological triplicates). Table S2: Total sRNA sequencing reads mapping to different sRNA producing RNA classes for control and cold treated samples. Table S3: sRNA size distribution in reads per million. The size distribution of total sRNAs derived from control and cold treated samples after adapter trimming.
DOI: 10.6084/m9.figshare.12586514
title: Additional file 6 of Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements

description: Additional files 6 to 12. Conserved locations of TIGD1 to TIGD7 in host vertebrate species and information about the upstream and downstream genes flanking them, retrieved from Ensembl [54]. Negative numbers indicate that the considered gene is upstream of the TIGD element.
DOI: 10.6084/m9.figshare.12586529
title: Additional file 12 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 12 Table S13: Differentially expressed sRNAs produced from non-overlapping lncRNAs. The sub-tables depict detailed sRNA and lncRNA transcript sequencing data at 3 h, 6 h and 2 d. Table S14: Differentially expressed sRNAs produced from cis-NAT pairs. The sub-tables depict detailed sRNA and cis-NAT sequencing data at 3 h, 6 h and 2 d. Table S15: Differentially expressed sRNAs produced from trans-NAT pairs. The sub-tables depict detailed sRNA and trans-NAT sequencing data at 3 h, 6 h and 2 d. Table S16: Differentially expressed sRNAs produced from PHAS pairs. The sub-tables depict detailed sRNA and PHAS transcript sequencing data at 3 h, 6 h and 2 d.
DOI: 10.6084/m9.figshare.12586508
title: Additional file 4 of Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements

description: Additional file 4. The amino acid alignment used to perform our phylogenetic analysis.
DOI: 10.6084/m9.figshare.12586511
title: Additional file 5 of Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements

description: Additional file 5. Fasta sequences of the 75 full-length Tc1/mariner elements used in this study.
DOI: 10.6084/m9.figshare.12586529.v1
title: Additional file 12 of Identification of small RNAs during cold acclimation in Arabidopsis thaliana

description: Additional file 12 Table S13: Differentially expressed sRNAs produced from non-overlapping lncRNAs. The sub-tables depict detailed sRNA and lncRNA transcript sequencing data at 3 h, 6 h and 2 d. Table S14: Differentially expressed sRNAs produced from cis-NAT pairs. The sub-tables depict detailed sRNA and cis-NAT sequencing data at 3 h, 6 h and 2 d. Table S15: Differentially expressed sRNAs produced from trans-NAT pairs. The sub-tables depict detailed sRNA and trans-NAT sequencing data at 3 h, 6 h and 2 d. Table S16: Differentially expressed sRNAs produced from PHAS pairs. The sub-tables depict detailed sRNA and PHAS transcript sequencing data at 3 h, 6 h and 2 d.
DOI: 10.6084/m9.figshare.12586505
title: Additional file 3 of Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements

description: Additional file 3. Alignment text files showing the DDD/E structure of each clade showing a conserved amino acid residues number between the second D and the third D or the E of the transposase domain. A) DDD/E alignment caption for HvSm and PlantMar. B) DDD alignment caption for TIGD1–4. C) DDD alignment caption for TIGD5–7.
DOI: 10.6084/m9.figshare.12586508.v1
title: Additional file 4 of Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements

description: Additional file 4. The amino acid alignment used to perform our phylogenetic analysis.
DOI: 10.6084/m9.figshare.12586514.v1
title: Additional file 6 of Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements

description: Additional files 6 to 12. Conserved locations of TIGD1 to TIGD7 in host vertebrate species and information about the upstream and downstream genes flanking them, retrieved from Ensembl [54]. Negative numbers indicate that the considered gene is upstream of the TIGD element.
DOI: 10.6084/m9.figshare.12586505.v1
title: Additional file 3 of Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements

description: Additional file 3. Alignment text files showing the DDD/E structure of each clade showing a conserved amino acid residues number between the second D and the third D or the E of the transposase domain. A) DDD/E alignment caption for HvSm and PlantMar. B) DDD alignment caption for TIGD1–4. C) DDD alignment caption for TIGD5–7.
DOI: 10.6084/m9.figshare.12586511.v1
title: Additional file 5 of Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements

description: Additional file 5. Fasta sequences of the 75 full-length Tc1/mariner elements used in this study.
DOI: 10.6084/m9.figshare.12586490
title: Additional file 7 of Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements

description: Additional File 13. The amino acid alignment used to perform the TIGD1–TIGD7 phylogenetic analysis.
DOI: 10.6084/m9.figshare.12586411
title: Additional file 2 of Counterbalancing the time-dependent effect on the human mitochondrial DNA molecular clock

description: Additional file 2 Supplementary tables: Table S1. Data from Figure S1 mtDNA African tree to calculate the human most recent common ancestor (TMRCA). Table S2. Age of the African mtDNA most recent common ancestor. Table S3. Age of the mtDNA haplogroup L3’4 split. Table S4. Age of the mtDNA L3 African expansion. Table S5. Data from Figure S2 mtDNA haplogroup P tree to calculate the Pacific human most recent common ancestor (TMRCA). Table S6. Age of the Pacific mtDNA haplogroup P most recent common ancestor. Table S7. Age of the mtDNA haplogroup P colonization of Australia. Table S8. Age of the mtDNA haplogroup P colonization of the Philippines. Table S9. Age of the mtDNA haplogroup P colonization of New Guinea. Table S10. Data from Figure S3 mtDNA American haplogroup B2 tree to calculate the Americas colonization age. Table S11. Age of the mtDNA haplogroup B2 colonization of the Americas.
DOI: 10.6084/m9.figshare.12586411.v1
title: Additional file 2 of Counterbalancing the time-dependent effect on the human mitochondrial DNA molecular clock

description: Additional file 2 Supplementary tables: Table S1. Data from Figure S1 mtDNA African tree to calculate the human most recent common ancestor (TMRCA). Table S2. Age of the African mtDNA most recent common ancestor. Table S3. Age of the mtDNA haplogroup L3’4 split. Table S4. Age of the mtDNA L3 African expansion. Table S5. Data from Figure S2 mtDNA haplogroup P tree to calculate the Pacific human most recent common ancestor (TMRCA). Table S6. Age of the Pacific mtDNA haplogroup P most recent common ancestor. Table S7. Age of the mtDNA haplogroup P colonization of Australia. Table S8. Age of the mtDNA haplogroup P colonization of the Philippines. Table S9. Age of the mtDNA haplogroup P colonization of New Guinea. Table S10. Data from Figure S3 mtDNA American haplogroup B2 tree to calculate the Americas colonization age. Table S11. Age of the mtDNA haplogroup B2 colonization of the Americas.
DOI: 10.6084/m9.figshare.12586408
title: Additional file 1 of Counterbalancing the time-dependent effect on the human mitochondrial DNA molecular clock

description: Additional file 1: Supplementary figures: Figure S1. Phylogenetic tree of mtDNA macrohaplogroup L complete African sequences produced in this study. Figure S2. MtDNA haplogroup P phylogeny. Figure S3. MtDNA haplogroup B2 phylogeny.