cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16551147.v1
title: Additional file 8 of The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments

description: Additional file 8 Expanded or contracted Artemia and H. dujardini orthogroups compared to other Arthropoda. Listed: Orthogroup ID, number of genes in this orthogroup in A. franciscana and in the other arthropod species, expanded or contracted status of the orthogroup in Artemia compared to the other arthropod species, comma-separated IPR description of Artemia genes in this orthogroup, H. dujardini genes in this orthogroup, Artemia genes in this orthogroup.
DOI: 10.6084/m9.figshare.16551150
title: Additional file 9 of The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments

description: Additional file 9. STAR mapping statistics for differential expression analysis in Artemia. Listed: sample name, total number of reads for this sample, percentage of uniquely mapped reads, absolute number of uniquely mapped reads, percentage of multi mapped reads, absolute number of multi mapped reads.
DOI: 10.6084/m9.figshare.16551150.v1
title: Additional file 9 of The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments

description: Additional file 9. STAR mapping statistics for differential expression analysis in Artemia. Listed: sample name, total number of reads for this sample, percentage of uniquely mapped reads, absolute number of uniquely mapped reads, percentage of multi mapped reads, absolute number of multi mapped reads.
DOI: 10.6084/m9.figshare.16551189
title: Additional file 3 of Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae

description: Additional file 3. Python script. Python script that was used to mine individual de novo transcriptomes for single-copy genes located through local BLAST databases. This script reads BLAST input files in XML format and extracts and translates a scaffold in all six reading frames based on the scaffold ID of the first BLAST hit. Once the scaffold is translated in all six reading frames, the ‘hit sequence’ is located and written to a file with the ‘query sequence’ in FASTA format.
DOI: 10.6084/m9.figshare.16551189.v1
title: Additional file 3 of Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae

description: Additional file 3. Python script. Python script that was used to mine individual de novo transcriptomes for single-copy genes located through local BLAST databases. This script reads BLAST input files in XML format and extracts and translates a scaffold in all six reading frames based on the scaffold ID of the first BLAST hit. Once the scaffold is translated in all six reading frames, the ‘hit sequence’ is located and written to a file with the ‘query sequence’ in FASTA format.
DOI: 10.6084/m9.figshare.16551205
title: Additional file 1 of Altered synthesis of genes associated with short-chain fatty acids in the gut of patients with atrial fibrillation

description: Additional file 1: Supplementary Table S1. The list of SCFA-related KOs.
DOI: 10.6084/m9.figshare.16551208
title: Additional file 2 of Altered synthesis of genes associated with short-chain fatty acids in the gut of patients with atrial fibrillation

description: Additional file 2: SupplementaryTable S2. Spearman correlation among 10 species that harbored synthesis enzyme genes for the SCFAs-related compounds.
DOI: 10.6084/m9.figshare.16551205.v1
title: Additional file 1 of Altered synthesis of genes associated with short-chain fatty acids in the gut of patients with atrial fibrillation

description: Additional file 1: Supplementary Table S1. The list of SCFA-related KOs.
DOI: 10.6084/m9.figshare.16551208.v1
title: Additional file 2 of Altered synthesis of genes associated with short-chain fatty acids in the gut of patients with atrial fibrillation

description: Additional file 2: SupplementaryTable S2. Spearman correlation among 10 species that harbored synthesis enzyme genes for the SCFAs-related compounds.
DOI: 10.6084/m9.figshare.16551225.v1
title: Additional file 3 of SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities

description: Additional file 2: Table S1. 16S rRNA gene-targeted group-specific primers. Table lists primer sets that already published and validated in the literature. All primers were used on mouse faeces samples apart from Alphaproteobacterial specific primers that were used on marine biofilm samples.
DOI: 10.6084/m9.figshare.16551225
title: Additional file 3 of SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities

description: Additional file 2: Table S1. 16S rRNA gene-targeted group-specific primers. Table lists primer sets that already published and validated in the literature. All primers were used on mouse faeces samples apart from Alphaproteobacterial specific primers that were used on marine biofilm samples.
DOI: 10.6084/m9.figshare.16551228.v1
title: Additional file 4 of SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities

description: Additional file 3: Table S2. First round PCR primers used for the first round of NGS library preparation.
DOI: 10.6084/m9.figshare.16551231
title: Additional file 5 of SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities

description: Additional file 4. Table S3 Second round PCR primers used for the first round of NGS library preparation.
DOI: 10.6084/m9.figshare.16551228
title: Additional file 4 of SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities

description: Additional file 3: Table S2. First round PCR primers used for the first round of NGS library preparation.
DOI: 10.6084/m9.figshare.16551234
title: Additional file 6 of SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities

description: Additional file 5: Table S4. OTUs prevalence analysis by sub-setting full dataset into multiple core OTUs. The table summarises the number OTUs within each subset dataset (subset by the % of samples that share OTUs) and percentage of the total number of OTUs within the full dataset (100%). This table also shows the number of reads and the percentage of total reads (100%) within each of the subset datasets. Note: in the 60% subset three samples were lost as they did not retain any under that criteria OTUs: Id-val1-PC1, Id-Val2-MG4 and Id-Val2-PC1.
DOI: 10.6084/m9.figshare.16551231.v1
title: Additional file 5 of SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities

description: Additional file 4. Table S3 Second round PCR primers used for the first round of NGS library preparation.
DOI: 10.6084/m9.figshare.16551237
title: Additional file 7 of SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities

description: Additional file 6: Table S5. Bacterial group responses to feed change within different gut compartments in real salmon and SalmoSim based on qPCR data. The table summarises the Estimated Marginal Means output for each mixed-effect linear model run with different qPCR measured relative abundance values identifying the difference between real salmon and SalmoSim response to feed change (Fish meal to Fish meal free diet) within different gut compartments (S – stomach, PC – pyloric caeca, and MG – mid gut). P&gt;0.05 values identify no change in the bacterial group, p&lt;0.05 identifies decrease (Est is negative), and p&lt;0.05 identifies increase (Est is positive) in the relative abundance of target group after the feed change. Bold values identify similarities between SalmoSim and real salmon samples. The SalmoSim values used for this test involves stable SalmoSim time points: days 16, 18 and 20 (Fish meal diet – once bacterial communities adapted to the SalmoSim environment), and days 36, 38 and 40 (Fish meal free diet – once bacterial communities adapted to feed change).
DOI: 10.6084/m9.figshare.16551234.v1
title: Additional file 6 of SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities

description: Additional file 5: Table S4. OTUs prevalence analysis by sub-setting full dataset into multiple core OTUs. The table summarises the number OTUs within each subset dataset (subset by the % of samples that share OTUs) and percentage of the total number of OTUs within the full dataset (100%). This table also shows the number of reads and the percentage of total reads (100%) within each of the subset datasets. Note: in the 60% subset three samples were lost as they did not retain any under that criteria OTUs: Id-val1-PC1, Id-Val2-MG4 and Id-Val2-PC1.
DOI: 10.6084/m9.figshare.16551237.v1
title: Additional file 7 of SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities

description: Additional file 6: Table S5. Bacterial group responses to feed change within different gut compartments in real salmon and SalmoSim based on qPCR data. The table summarises the Estimated Marginal Means output for each mixed-effect linear model run with different qPCR measured relative abundance values identifying the difference between real salmon and SalmoSim response to feed change (Fish meal to Fish meal free diet) within different gut compartments (S – stomach, PC – pyloric caeca, and MG – mid gut). P&gt;0.05 values identify no change in the bacterial group, p&lt;0.05 identifies decrease (Est is negative), and p&lt;0.05 identifies increase (Est is positive) in the relative abundance of target group after the feed change. Bold values identify similarities between SalmoSim and real salmon samples. The SalmoSim values used for this test involves stable SalmoSim time points: days 16, 18 and 20 (Fish meal diet – once bacterial communities adapted to the SalmoSim environment), and days 36, 38 and 40 (Fish meal free diet – once bacterial communities adapted to feed change).
DOI: 10.6084/m9.figshare.16551238
title: Additional file 2 of Single-cell analysis of cell fate bifurcation in the chordate Ciona

description: Additional File 2: Table S1 - Sequencing statistics. Table S2 - Number of stamps in each cluster for all treatments and developmental stages. Table S3 - Marker genes for all clusters at the 112-cell stage. Table S4 - Transcription factor differential expression in “trios”. Table S5 - GO code enrichment for Biological Process terms in notochord waves. Table S6 - Transcription factor association with open chromatin length in Ciona. Table S7 - Effector TFs associated with putative Ciona super-enhancers.
DOI: 10.6084/m9.figshare.16551238.v1
title: Additional file 2 of Single-cell analysis of cell fate bifurcation in the chordate Ciona

description: Additional File 2: Table S1 - Sequencing statistics. Table S2 - Number of stamps in each cluster for all treatments and developmental stages. Table S3 - Marker genes for all clusters at the 112-cell stage. Table S4 - Transcription factor differential expression in “trios”. Table S5 - GO code enrichment for Biological Process terms in notochord waves. Table S6 - Transcription factor association with open chromatin length in Ciona. Table S7 - Effector TFs associated with putative Ciona super-enhancers.
DOI: 10.6084/m9.figshare.13533215
title: Additional file 1 of Phlebotomus (Adlerius) simici NITZULESCU, 1931: first record in Austria and phylogenetic relationship with other Adlerius species

description: Additional file 1: Table S1. Included coxI sequences of Adlerius spp. for pairwise distance calculations.
DOI: 10.6084/m9.figshare.13533215.v1
title: Additional file 1 of Phlebotomus (Adlerius) simici NITZULESCU, 1931: first record in Austria and phylogenetic relationship with other Adlerius species

description: Additional file 1: Table S1. Included coxI sequences of Adlerius spp. for pairwise distance calculations.
DOI: 10.6084/m9.figshare.13533218.v1
title: Additional file 2 of Phlebotomus (Adlerius) simici NITZULESCU, 1931: first record in Austria and phylogenetic relationship with other Adlerius species

description: Additional file 2: Table S2. Pairwise distances (%) of coxI based on Tamura’s 3-parameter model with 1000 bootstrap values. Description in brackets refer to the respective haplotype in the network. Standard errors are shown in blue.
DOI: 10.6084/m9.figshare.13533221
title: Additional file 3 of Phlebotomus (Adlerius) simici NITZULESCU, 1931: first record in Austria and phylogenetic relationship with other Adlerius species

description: Additional file 3: Table S3. Included cytb sequences of Adlerius spp. for pairwise distance calculations.
DOI: 10.6084/m9.figshare.13533218
title: Additional file 2 of Phlebotomus (Adlerius) simici NITZULESCU, 1931: first record in Austria and phylogenetic relationship with other Adlerius species

description: Additional file 2: Table S2. Pairwise distances (%) of coxI based on Tamura’s 3-parameter model with 1000 bootstrap values. Description in brackets refer to the respective haplotype in the network. Standard errors are shown in blue.
DOI: 10.6084/m9.figshare.13533221.v1
title: Additional file 3 of Phlebotomus (Adlerius) simici NITZULESCU, 1931: first record in Austria and phylogenetic relationship with other Adlerius species

description: Additional file 3: Table S3. Included cytb sequences of Adlerius spp. for pairwise distance calculations.
DOI: 10.6084/m9.figshare.13533224
title: Additional file 4 of Phlebotomus (Adlerius) simici NITZULESCU, 1931: first record in Austria and phylogenetic relationship with other Adlerius species

description: Additional file 4: Table S4. Pairwise distances (%) of cytb based on Tamura–Nei’s parameter model with 1000 bootstrap values. Description in brackets refer to the respective haplotype in the network. Standard errors are shown in blue.
DOI: 10.6084/m9.figshare.13533224.v1
title: Additional file 4 of Phlebotomus (Adlerius) simici NITZULESCU, 1931: first record in Austria and phylogenetic relationship with other Adlerius species

description: Additional file 4: Table S4. Pairwise distances (%) of cytb based on Tamura–Nei’s parameter model with 1000 bootstrap values. Description in brackets refer to the respective haplotype in the network. Standard errors are shown in blue.
DOI: 10.6084/m9.figshare.16551325
title: Additional file 2 of Predictability of polygenic risk score for progression to dementia and its interaction with APOE ε4 in mild cognitive impairment

description: Additional file 2: Table S3. List of mapped genes.
DOI: 10.6084/m9.figshare.16551325.v1
title: Additional file 2 of Predictability of polygenic risk score for progression to dementia and its interaction with APOE ε4 in mild cognitive impairment

description: Additional file 2: Table S3. List of mapped genes.
DOI: 10.6084/m9.figshare.16551352
title: Additional file 2 of Transmission patterns of rifampicin resistant Mycobacterium tuberculosis complex strains in Cameroon: a genomic epidemiological study

description: Additional file 2: Table S1. Molecular and phenotypic data of MTBC isolates from 195 RR/MDR-TB patients in Cameroon (2013–2015) including patient characteristics.
DOI: 10.6084/m9.figshare.16551352.v1
title: Additional file 2 of Transmission patterns of rifampicin resistant Mycobacterium tuberculosis complex strains in Cameroon: a genomic epidemiological study

description: Additional file 2: Table S1. Molecular and phenotypic data of MTBC isolates from 195 RR/MDR-TB patients in Cameroon (2013–2015) including patient characteristics.
DOI: 10.6084/m9.figshare.16551355
title: Additional file 3 of Transmission patterns of rifampicin resistant Mycobacterium tuberculosis complex strains in Cameroon: a genomic epidemiological study

description: Additional file 3: Table S2. Contact tracing data of patients in molecular clusters and pyrazinamide resistance conferring mutations in pncA.
DOI: 10.6084/m9.figshare.16551355.v1
title: Additional file 3 of Transmission patterns of rifampicin resistant Mycobacterium tuberculosis complex strains in Cameroon: a genomic epidemiological study

description: Additional file 3: Table S2. Contact tracing data of patients in molecular clusters and pyrazinamide resistance conferring mutations in pncA.
DOI: 10.6084/m9.figshare.16551330
title: Additional file 10 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 10: Table S9. Differential H3K27me3 peaks in h2a_ub and Mpbmi1/1l mutants.
DOI: 10.6084/m9.figshare.16551330.v1
title: Additional file 10 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 10: Table S9. Differential H3K27me3 peaks in h2a_ub and Mpbmi1/1l mutants.
DOI: 10.6084/m9.figshare.16551336
title: Additional file 11 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 11: Table S10. Arabidopsis homologs of Marchantia genes.
DOI: 10.6084/m9.figshare.16551336.v1
title: Additional file 11 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 11: Table S10. Arabidopsis homologs of Marchantia genes.
DOI: 10.6084/m9.figshare.16551345
title: Additional file 2 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 2: Table S1. Primers used in the constructs.
DOI: 10.6084/m9.figshare.16551345.v1
title: Additional file 2 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 2: Table S1. Primers used in the constructs.
DOI: 10.6084/m9.figshare.16551348
title: Additional file 3 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 3: Table S2. Mapping statistics of RNA-seq data.
DOI: 10.6084/m9.figshare.16551348.v1
title: Additional file 3 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 3: Table S2. Mapping statistics of RNA-seq data.
DOI: 10.6084/m9.figshare.16551351
title: Additional file 4 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 4: Table S3. Genes deregulated in h2a_ub and Mpbmi1/1l mutants.
DOI: 10.6084/m9.figshare.16551351.v1
title: Additional file 4 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 4: Table S3. Genes deregulated in h2a_ub and Mpbmi1/1l mutants.
DOI: 10.6084/m9.figshare.16551354
title: Additional file 5 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 5: Table S4. TEs deregulated in h2a_ub and Mpbmi1/1l mutants.
DOI: 10.6084/m9.figshare.16551354.v1
title: Additional file 5 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 5: Table S4. TEs deregulated in h2a_ub and Mpbmi1/1l mutants.
DOI: 10.6084/m9.figshare.16551357
title: Additional file 6 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 6: Table S5. Mapping statistics of ChIP-seq data.
DOI: 10.6084/m9.figshare.16551357.v1
title: Additional file 6 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 6: Table S5. Mapping statistics of ChIP-seq data.
DOI: 10.6084/m9.figshare.16551360
title: Additional file 7 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 7: Table S6. Three specified group of genes defined by H2Aub and H3K27me3 marks.
DOI: 10.6084/m9.figshare.16551360.v1
title: Additional file 7 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 7: Table S6. Three specified group of genes defined by H2Aub and H3K27me3 marks.
DOI: 10.6084/m9.figshare.16551363
title: Additional file 8 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 8: Table S7. TEs marked by H2Aub and H3K27me3.
DOI: 10.6084/m9.figshare.16551363.v1
title: Additional file 8 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 8: Table S7. TEs marked by H2Aub and H3K27me3.
DOI: 10.6084/m9.figshare.16551366
title: Additional file 9 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 9: Table S8. Differential H2Aub peaks in h2a_ub and Mpbmi1/1l mutants.
DOI: 10.6084/m9.figshare.16551366.v1
title: Additional file 9 of H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

description: Additional file 9: Table S8. Differential H2Aub peaks in h2a_ub and Mpbmi1/1l mutants.
DOI: 10.25345/c5nc2z
title: MassIVE MSV000088040 - Mono-Colonized GF Reporter Mice
title: Mono-colonized GF reporter mice fecal metabolomics by LC-MS/MS
DOI: 10.5281/zenodo.5348591
title: Visualizing the organization and differentiation of the male-specific nervous system of C. elegans

description: Image volumes and annotations for male NeuroPAL, flp-3, flp-27, and nlp-51 expression. The following image volumes were annotated by Tessa Tekieli, Chen Wang, and Robert Fernandez for:<br> "Visualizing the organization and differentiation of the male-specific nervous system of C. elegans". The publication is available here:<br> https://journals.biologists.com/dev/article-abstract/doi/10.1242/dev.199687/271902/Visualizing-the-organization-and-differentiation These image files can be viewed with the NeuroPAL ID software, available at:<br> https://www.hobertlab.org/neuropal/<br> OR<br> https://github.com/amin-nejat/CELL_ID This software was provided for the NeuroPAL publication, "NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. <em>elegans</em>".<br> The publication is available here:<br> https://www.cell.com/cell/fulltext/S0092-8674(20)31682-2 Please cite the NeuroPAL publication when using the software.