cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11776413.v2
title: Datasets (raw and true reads) supporting the study "Benchmarking of computational error-correction methods for next-generation sequencing data"

description: We used both simulated and experimental datasets derived from human genomic DNA, human T cell receptor repertoires, and intra-host viral populations. Next, we summarize datasets shared here, i.e., D1, D2, D3, D4, and D5. More details can be found in our paper.<b><br></b><b>D1 dataset:</b> D1 was produced by computational simulations using a customized version of the tool WgSim. We generated simulated data mimicking the WGS human data using a customized version of the tool WgSim. Read coverage varied between 1 and 32. The WgSim fork is available at https://github.com/mandricigor/wgsim. <b><br></b><b>D2 dataset:</b> Raw reads corresponding to 8 samples (SRR1543964, SRR1543965, SRR1543966, SRR1543967, SRR1543968, SRR1543969, SRR1543970, and SRR1543971) were downloaded from https://www.ncbi.nlm.nih.gov/. The error-free (true) reads for the D2 dataset were generated using a UMI-based high-fidelity sequencing protocol, also known as safe-SeqS.<b><br></b><b>D3 dataset:</b> We generated simulated data mimicking the TCR-Seq data using the T cell receptor alpha chain (TCRA). Samples have read lengths of 100bp and read coverage varied between 1 and 32. <br><b>D4 dataset:</b> D4 corresponds to HIV population sequencing of an infected patient. The error-free (true) reads for the D4 dataset were generated using a UMI-based high-fidelity sequencing protocol.<br><br><b>D5 dataset:</b> We prepared the viral dataset D5 using real sequencing data from NCBI with the accession number SRR961514. Each read was assigned to the reference with which it has a minimum number of mismatches. The original error rate in the dataset was 1.44%. We modified these reads as follows: first, we corrected the corresponding portion of errors with a corresponding reference nucleotides to obtain different levels of errors in the datasets (1.44%, 0.33%, 0.1%, 0.033%, 0.01% , 0.0033%, 0.001%, 0.00033%, 0.0001%); We also created datasets with mixtures of two haplotypes with the original 1.44% error rate but with different levels of diversity between haplotypes (Hamming distance=5.94%, 0.29%, 0.02%). We applied a haplotype-based error correction protocol to eliminate sequencing errors from the D5 dataset.<br>For more information, please visit our main repository:https://github.com/Mangul-Lab-USC/benchmarking.error.correction. <br><br>
DOI: 10.6084/m9.figshare.11776404.v1
title: The effect of oxidation state of metal on electrochemical and photochemical driven hydrogen evolution catalyzed by nickel complexes of maleonitriledithiolate ligands

description: Two nickel-based catalysts, TBA<sub>2</sub>[Ni<sup>II</sup>(mnt)<sub>2</sub>] <b>1</b> and TBA[Ni<sup>III</sup>(mnt)<sub>2</sub>] <b>2</b> are formed by the reactions of NiCl<sub>2</sub>·6H<sub>2</sub>O, Na<sub>2</sub>(mnt), and tetra-n-butylammoniumbromide (TBABr) without or with iodine (I<sub>2</sub>) (mnt = 2,2-dicyanoethylene-1,1-dithiolate), respectively. Under an overpotential (OP) of 941.6 mV, complexes <b>1</b> and <b>2</b> can electrocatalyze hydrogen evolution from acetic acid with a turnover frequency (TOF) of 36.3 and 148.31 mol H<sub>2</sub>/mol catalyst/h, respectively. Under blue light (<i>λ</i><sub>max</sub> = 469 nm), <b>1</b> or <b>2</b>, together with CdS nanorods (CdS NRs) as a photosensitizer, and ascorbic acid (H<sub>2</sub>A) as a sacrificial electron donor, can produce hydrogen with a turnover number (TON) of 7760 and 17,570 moles of H<sub>2</sub> per mole of catalyst during 35 h irradiation, respectively. The average value of apparent quantum yield (AQY) is ∼9.2% (complex <b>1</b>) and 28% (complex <b>2</b>), respectively. The results indicate that the nickel(III) complex has a better active activity for hydrogen production than the nickel(II) species.
DOI: 10.6084/m9.figshare.11776287
title: Additional file 3 of Genetic segregation for male body coloration and female mate preference in the guppy

description: Additional file 3. Data list of male orange area and female preference. Data of all individuals for which male orange area and female preference was measured.
DOI: 10.6084/m9.figshare.11776287.v1
title: Additional file 3 of Genetic segregation for male body coloration and female mate preference in the guppy

description: Additional file 3. Data list of male orange area and female preference. Data of all individuals for which male orange area and female preference was measured.
DOI: 10.6084/m9.figshare.11776278
title: Additional file 2 of Detection of suspicious interactions of spiking covariates in methylation data

description: Additional file 2 R code and example of the Algorithms 1 and 2 for the detection of suspicious spike interactions.
DOI: 10.6084/m9.figshare.11776278.v1
title: Additional file 2 of Detection of suspicious interactions of spiking covariates in methylation data

description: Additional file 2 R code and example of the Algorithms 1 and 2 for the detection of suspicious spike interactions.
DOI: 10.6084/m9.figshare.11776206
title: Additional file 14 of Transcriptomics supports local sensory regulation in the antenna of the kissing-bug Rhodnius prolixus

description: Additional file 14: Data file S3. Edited Generic Feature Format (GFF) file of the R. prolixus genome used for read mapping and gene expression analysis.
DOI: 10.6084/m9.figshare.11776206.v1
title: Additional file 14 of Transcriptomics supports local sensory regulation in the antenna of the kissing-bug Rhodnius prolixus

description: Additional file 14: Data file S3. Edited Generic Feature Format (GFF) file of the R. prolixus genome used for read mapping and gene expression analysis.
DOI: 10.6084/m9.figshare.11776131
title: Additional file 2 of Blood signatures for second stage human African trypanosomiasis: a transcriptomic approach

description: Additional file 2: Table S1. Cases vs Controls DEGs. Table S2. Cases vs Controls - Immune response gene enrichment. Table S3. Cases vs CSF DEGs. Table S4. Cases vs CSF - Gene functional annotation. Table S5. DEGs in the blood and CSF during active infection.
DOI: 10.6084/m9.figshare.11776131.v1
title: Additional file 2 of Blood signatures for second stage human African trypanosomiasis: a transcriptomic approach

description: Additional file 2: Table S1. Cases vs Controls DEGs. Table S2. Cases vs Controls - Immune response gene enrichment. Table S3. Cases vs CSF DEGs. Table S4. Cases vs CSF - Gene functional annotation. Table S5. DEGs in the blood and CSF during active infection.
DOI: 10.6084/m9.figshare.11776122
title: Additional file 8 of Identification of eQTLs and sQTLs associated with meat quality in beef

description: Additional file 8. Bonferroni cis thresholds by gene. The number of tests, number of effective tests and the Bonferroni adjusted p-value is presented by each gene used in the association analysis.
DOI: 10.6084/m9.figshare.11776122.v1
title: Additional file 8 of Identification of eQTLs and sQTLs associated with meat quality in beef

description: Additional file 8. Bonferroni cis thresholds by gene. The number of tests, number of effective tests and the Bonferroni adjusted p-value is presented by each gene used in the association analysis.
DOI: 10.6084/m9.figshare.11776113
title: Additional file 7 of Identification of eQTLs and sQTLs associated with meat quality in beef

description: Additional file 7. List of DEG and expressed genes. A list of 1352 genes considered as DEG genes for meat quality in the present analysis, and 8799 genes identified as expressed in longissimus dorsi muscle in a multibreed Angus-Brahman herd.
DOI: 10.6084/m9.figshare.11776113.v1
title: Additional file 7 of Identification of eQTLs and sQTLs associated with meat quality in beef

description: Additional file 7. List of DEG and expressed genes. A list of 1352 genes considered as DEG genes for meat quality in the present analysis, and 8799 genes identified as expressed in longissimus dorsi muscle in a multibreed Angus-Brahman herd.
DOI: 10.6084/m9.figshare.11776104
title: Additional file 6 of Identification of eQTLs and sQTLs associated with meat quality in beef

description: Additional file 6. Enriched terms identified by DAVID Bioinformatic Resources 6.8 server functional classification analysis. These terms were found enriched when performing analysis inside each expression or splicing master regulator cluster, or across regulated genes. The QTL mapping was performed in longissimus dorsi muscle sampled from a multibreed Angus-Brahman herd.
DOI: 10.6084/m9.figshare.11776104.v1
title: Additional file 6 of Identification of eQTLs and sQTLs associated with meat quality in beef

description: Additional file 6. Enriched terms identified by DAVID Bioinformatic Resources 6.8 server functional classification analysis. These terms were found enriched when performing analysis inside each expression or splicing master regulator cluster, or across regulated genes. The QTL mapping was performed in longissimus dorsi muscle sampled from a multibreed Angus-Brahman herd.
DOI: 10.6084/m9.figshare.11776095
title: Additional file 4 of Identification of eQTLs and sQTLs associated with meat quality in beef

description: Additional file 4. List of 231 regulated genes and their respective splicing master regulators identified by the sQTL association mapping. The sQTL mapping was performed in longissimus dorsi muscle sampled from a multibreed Angus-Brahman herd. SNP information about 112,042 markers and expression data from 87,770 exons (8467 genes) were included in the association assay
DOI: 10.6084/m9.figshare.11776095.v1
title: Additional file 4 of Identification of eQTLs and sQTLs associated with meat quality in beef

description: Additional file 4. List of 231 regulated genes and their respective splicing master regulators identified by the sQTL association mapping. The sQTL mapping was performed in longissimus dorsi muscle sampled from a multibreed Angus-Brahman herd. SNP information about 112,042 markers and expression data from 87,770 exons (8467 genes) were included in the association assay
DOI: 10.6084/m9.figshare.11776080
title: Additional file 2 of Identification of eQTLs and sQTLs associated with meat quality in beef

description: Additional file 2. List of 674 regulated genes and their respective expression master regulator identified by the eQTL association mapping. The eQTL mapping was performed in longissimus dorsi muscle sampled from a multibreed Angus-Brahman herd. SNP information about 112,042 markers and expression data from 8588 genes were included in the association assay.
DOI: 10.6084/m9.figshare.11776080.v1
title: Additional file 2 of Identification of eQTLs and sQTLs associated with meat quality in beef

description: Additional file 2. List of 674 regulated genes and their respective expression master regulator identified by the eQTL association mapping. The eQTL mapping was performed in longissimus dorsi muscle sampled from a multibreed Angus-Brahman herd. SNP information about 112,042 markers and expression data from 8588 genes were included in the association assay.
DOI: 10.6084/m9.figshare.11776074
title: Additional file 1 of Identification of eQTLs and sQTLs associated with meat quality in beef

description: Additional file 1. Cis eQTL and sQTL effects identified in longissimus dorsi muscle sampled from a multibreed Angus-Brahman herd. SNP information about 112,042 markers and expression data from 8588 genes and 87,770 exons from 8467 genes were included in the association assay. Out of the 8588 genes included, expression of 1352 loci was previously identified as related to meat quality traits and denoted as DEG genes.
DOI: 10.6084/m9.figshare.11776074.v1
title: Additional file 1 of Identification of eQTLs and sQTLs associated with meat quality in beef

description: Additional file 1. Cis eQTL and sQTL effects identified in longissimus dorsi muscle sampled from a multibreed Angus-Brahman herd. SNP information about 112,042 markers and expression data from 8588 genes and 87,770 exons from 8467 genes were included in the association assay. Out of the 8588 genes included, expression of 1352 loci was previously identified as related to meat quality traits and denoted as DEG genes.
DOI: 10.6084/m9.figshare.11776056
title: Additional file 4 of Analytical characterization of trace elements (zinc, copper, cadmium, lead and selenium) in saliva of pigs under common pathological conditions in the field: a pilot study

description: Additional file 4: Raw data of all the measurements performed in saliva samples of healthy pigs from farm 2.
DOI: 10.6084/m9.figshare.11776056.v1
title: Additional file 4 of Analytical characterization of trace elements (zinc, copper, cadmium, lead and selenium) in saliva of pigs under common pathological conditions in the field: a pilot study

description: Additional file 4: Raw data of all the measurements performed in saliva samples of healthy pigs from farm 2.
DOI: 10.6084/m9.figshare.11776047
title: Additional file 3 of Analytical characterization of trace elements (zinc, copper, cadmium, lead and selenium) in saliva of pigs under common pathological conditions in the field: a pilot study

description: Additional file 3: Raw data of the Hp, CRP, TAC and ADA concentrations measured in saliva samples of pigs under clinical conditions.
DOI: 10.6084/m9.figshare.11776047.v1
title: Additional file 3 of Analytical characterization of trace elements (zinc, copper, cadmium, lead and selenium) in saliva of pigs under common pathological conditions in the field: a pilot study

description: Additional file 3: Raw data of the Hp, CRP, TAC and ADA concentrations measured in saliva samples of pigs under clinical conditions.
DOI: 10.6084/m9.figshare.11776035
title: Additional file 1 of Analytical characterization of trace elements (zinc, copper, cadmium, lead and selenium) in saliva of pigs under common pathological conditions in the field: a pilot study

description: Additional file 1: Raw data of the analytical validation study performed for trace elements measurements in saliva of pigs.
DOI: 10.6084/m9.figshare.11776038
title: Additional file 2 of Analytical characterization of trace elements (zinc, copper, cadmium, lead and selenium) in saliva of pigs under common pathological conditions in the field: a pilot study

description: Additional file 2: Raw data of the trace elements measured in saliva samples of pigs under clinical condition.
DOI: 10.6084/m9.figshare.11776038.v1
title: Additional file 2 of Analytical characterization of trace elements (zinc, copper, cadmium, lead and selenium) in saliva of pigs under common pathological conditions in the field: a pilot study

description: Additional file 2: Raw data of the trace elements measured in saliva samples of pigs under clinical condition.
DOI: 10.6084/m9.figshare.11776035.v1
title: Additional file 1 of Analytical characterization of trace elements (zinc, copper, cadmium, lead and selenium) in saliva of pigs under common pathological conditions in the field: a pilot study

description: Additional file 1: Raw data of the analytical validation study performed for trace elements measurements in saliva of pigs.
DOI: 10.6084/m9.figshare.11775957
title: Additional file 1 of Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress

description: Additional file 1: Table S1. List of the NAC sequences in broomcorn millet. Table S2. Protein property of PmNAC proteins. Table S3. The structural features of motif 1â€“20. Table S4. Expression (FPKM) of PmNAC genes in different tissues. Table S5. Expression (FPKM) of PmNAC genes in response to drought treatment in broomcorn millet. Table S6. The gene ID of NAC members from Arabidopsis thaliana. Table S7. Sequences of primers used in qRT-PCR.
DOI: 10.6084/m9.figshare.11775957.v1
title: Additional file 1 of Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress

description: Additional file 1: Table S1. List of the NAC sequences in broomcorn millet. Table S2. Protein property of PmNAC proteins. Table S3. The structural features of motif 1â€“20. Table S4. Expression (FPKM) of PmNAC genes in different tissues. Table S5. Expression (FPKM) of PmNAC genes in response to drought treatment in broomcorn millet. Table S6. The gene ID of NAC members from Arabidopsis thaliana. Table S7. Sequences of primers used in qRT-PCR.
DOI: 10.6073/pasta/5bf131bc3b03ec9f59dc885629065824
title: SBC LTER: Reef: Long-term experiment: Kelp removal: Abundance and size of Giant Kelp

description: These data describe the abundance of giant kelp located at SBC LTER long-term kelp removal experiment sites. The number of fronds on each plant &gt; 1 m tall within 40 m x 2 m transects in each plot is recorded in selected 20 m2 sub-sections of each transect. In continuous removal plots plants are removed after being sampled. The kelp removal experiment was initiated in 2008 at selected reef sites along the mainland coast of the Santa Barbara Channel. The following three giant kelp manipulations are maintained in sampling plots at each site: - Control: Macrocystis pyriferais left intact in a 2000 m2 plot. - Annual removal: Macrocystis pyriferais removed from an adjacent 2000 m2 plot once each winter and allowed to re-colonize over the course of the year. - Continuous removal: Macrocystis pyriferais removed from a 200 m2 area within the 2000 m2 plot on each sampling date. See Methods for more information.
DOI: 10.6084/m9.figshare.11775867
title: Additional file 2 of The effects of common structural variants on 3D chromatin structure

description: Additional file 2: Table S1. Summary statistics for all common deletions. 2180 common deletions from 19 individuals in the 1000 Genomes Project were annotated with TAD boundaries, eQTLs, and GWAS hits. To investigate the effect of these deletions on chromatin conformation, a linear regression was performed between genotype and the median number of chromatin interactions within the flank and span region of each deletion. Ancestry principal components and sex were used as covariates in the regression model
DOI: 10.6084/m9.figshare.11775867.v1
title: Additional file 2 of The effects of common structural variants on 3D chromatin structure

description: Additional file 2: Table S1. Summary statistics for all common deletions. 2180 common deletions from 19 individuals in the 1000 Genomes Project were annotated with TAD boundaries, eQTLs, and GWAS hits. To investigate the effect of these deletions on chromatin conformation, a linear regression was performed between genotype and the median number of chromatin interactions within the flank and span region of each deletion. Ancestry principal components and sex were used as covariates in the regression model
DOI: 10.6084/m9.figshare.11775837
title: Additional file 2 of Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations

description: Additional file 2. Allele list.
DOI: 10.6084/m9.figshare.11775837.v1
title: Additional file 2 of Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations

description: Additional file 2. Allele list.
DOI: 10.6084/m9.figshare.11775834
title: Additional file 3 of Transcriptomic analysis of dead end knockout testis reveals germ cell and gonadal somatic factors in Atlantic salmon

description: Additional file 3. KEGG pathways. Full list of KEGG pathways annotated to gonad specific genes with expression preferentially within germ cells [Additional File 2] of adult Atlantic salmon males. Pathway ID, pathway, number of genes within each pathway, gene ID and symbol are shown
DOI: 10.6084/m9.figshare.11775834.v1
title: Additional file 3 of Transcriptomic analysis of dead end knockout testis reveals germ cell and gonadal somatic factors in Atlantic salmon

description: Additional file 3. KEGG pathways. Full list of KEGG pathways annotated to gonad specific genes with expression preferentially within germ cells [Additional File 2] of adult Atlantic salmon males. Pathway ID, pathway, number of genes within each pathway, gene ID and symbol are shown
DOI: 10.6084/m9.figshare.11775825
title: Additional file 2 of Transcriptomic analysis of dead end knockout testis reveals germ cell and gonadal somatic factors in Atlantic salmon

description: Additional file 2. Gonad specific genes with expression preferentially within germ cells. List of gonad specific (≤50 reads in extragonadal tissues and ≥ 100 reads in ovary and testis) genes with expression preferentially within germ cells (≤50 reads in germ cell-free testis and ≥ 100 reads in WT testis) of adult Atlantic salmon males. Transcript ID, Gene ID, number of reads in multiple tissues (brain, eye, gill, gut, head kidney, heart, kidney, liver, muscle, nose, pyloric caecum, skin, spleen, ovary, testis (GenBank GBRB00000000.1 [23]; (highlighted in grey)), and number of reads in juvenile wild type (WT) and dead end knockout (dnd-KO) testis tissue (highlighted in green) are shown
DOI: 10.6084/m9.figshare.11775822
title: Additional file 1 of Transcriptomic analysis of dead end knockout testis reveals germ cell and gonadal somatic factors in Atlantic salmon

description: Additional file 1. Gonad specific genes. List of gonad specific (≤50 reads in extragonadal tissues and ≥ 100 reads in ovary and testis) genes in adult Atlantic salmon. Transcript ID, Gene ID, number of reads in multiple tissues (brain, eye, gill, gut, head kidney, heart, kidney, liver, muscle, nose, pyloric caecum, skin, spleen, ovary, testis (GenBank GBRB00000000.1 [23];) are shown
DOI: 10.6084/m9.figshare.11775825.v1
title: Additional file 2 of Transcriptomic analysis of dead end knockout testis reveals germ cell and gonadal somatic factors in Atlantic salmon

description: Additional file 2. Gonad specific genes with expression preferentially within germ cells. List of gonad specific (≤50 reads in extragonadal tissues and ≥ 100 reads in ovary and testis) genes with expression preferentially within germ cells (≤50 reads in germ cell-free testis and ≥ 100 reads in WT testis) of adult Atlantic salmon males. Transcript ID, Gene ID, number of reads in multiple tissues (brain, eye, gill, gut, head kidney, heart, kidney, liver, muscle, nose, pyloric caecum, skin, spleen, ovary, testis (GenBank GBRB00000000.1 [23]; (highlighted in grey)), and number of reads in juvenile wild type (WT) and dead end knockout (dnd-KO) testis tissue (highlighted in green) are shown
DOI: 10.6084/m9.figshare.11775822.v1
title: Additional file 1 of Transcriptomic analysis of dead end knockout testis reveals germ cell and gonadal somatic factors in Atlantic salmon

description: Additional file 1. Gonad specific genes. List of gonad specific (≤50 reads in extragonadal tissues and ≥ 100 reads in ovary and testis) genes in adult Atlantic salmon. Transcript ID, Gene ID, number of reads in multiple tissues (brain, eye, gill, gut, head kidney, heart, kidney, liver, muscle, nose, pyloric caecum, skin, spleen, ovary, testis (GenBank GBRB00000000.1 [23];) are shown
DOI: 10.6084/m9.figshare.11775810
title: Additional file 3 of Periostin plays a critical role in the cell cycle in lung fibroblasts

description: Additional file 3: Table S2. The profile of genes downregulated to less than one third or upregulated by more than three-fold by knockdown of periostin using DNA microarrays.
DOI: 10.6084/m9.figshare.11775810.v1
title: Additional file 3 of Periostin plays a critical role in the cell cycle in lung fibroblasts

description: Additional file 3: Table S2. The profile of genes downregulated to less than one third or upregulated by more than three-fold by knockdown of periostin using DNA microarrays.
DOI: 10.6084/m9.figshare.11775780
title: Additional file 3 of Repetitive DNA content in the maize genome is uncoupled from population stratification at SNP loci

description: Additional file 3 Cluster read counts by inbred. A file listing cluster name and the number of reads from each inbred that contributed to the given cluster.