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zenodo44/100

Quartet of familiar females – 16p11.2 Del mouse strain – 2 WT + 2 Del/+ - F10

We monitored the individual and social behaviours of each quartet of mice over three days and nights in the Live Mouse Tracker system (LMT, plugin 931; de Chaumont et al. 2019 Nat. Biomed. Engin.). This system tracks individually mice living in a group over several days and nights and extracts automatically the number, total duration and mean duration of more than thirty behavioural events describing the posture of the mouse, the types of social contacts, the dynamic social approach and escapes and complex social groupings (see de Chaumont et al. 2019 Nat. Biomed. Engin.). In this system, the four mice (10-14 weeks of age; 2 WT mice and 2 Del/+ mice) from the same housing cage (housed together from weaning on) were left undisturbed for 71 hours in a large transparent Plexiglas cage (50 x 50 x 40 cm), with fresh bedding, a house (width: 100 mm, depth: 75 mm, height: 40 mm) in red Plexiglas, 6 dental cotton rolls as well as food and water ad libitum. Light/dark cycle and temperature conditions were similar to those of the housing room (12/12h light/dark, lights on at 07:00 AM, 100 lux when the lights were on). Each recording session started between 03:00 and 04:00 PM. At the end of the session, mice were placed back in their home cage and the LMT setup was cleaned with soap water and dried with paper towels. The upload includes the sqlite database from LMT (processed).

opencc-by-4.0Dec 2022View details →

zenodo44/100

Quartet of familiar females – 16p11.2 Del mouse strain – 2 WT + 2 Del/+ - F9

opencc-by-4.0Dec 2022View details →

zenodo44/100

Arthralgia in female Masters weightlifters

OVERVIEW 1. Title of Dataset: Arthralgia in female Master weightlifters 2. Author Information Name: Marianne Huebner Institution: Michigan State University Address: East Lansing, MI 48824 3. Period of data collection: 27 April – 20 May 2022 4. Geographic region of data collection: Online survey in USA with participants from 30 countries in IWF regions Africa, Asia, Europe, Oceania, PanAmerican LIST OF FILES Dataset: wlmeno_oa.csv Data dictionary: wlmeno_oa_meta.xlsx METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: The survey was distributed by the Master Committee of the International Weightlifting Federation (IWF) to the National Master Chairs. They then used email or social media to communicate the study to the women weightlifters. The Survey was available in four languages (English, German, French, Spanish), translated and tested by native speakers. In addition, the survey was advertised in weightlifting interest groups via Facebook and Instagram. The survey was administered online via Qualtrics (Provo, UT, USA). 2. Methods for processing the data: Data were downloaded from Qualtrics (Provo, UT, USA) to Excel and then pre-processed in the statistical software R v. 4.3.0. (<a href="https://www.r-project.org/">https://www.r-project.org</a>)  Variable formats (numeric, character) were checked and transformed, as appropriate. 3. Quality-assurance procedures performed on the data:  Exclusion criteria were younger than 30 years (n=1), currently pregnant (n=3). To account for the possibility of male participants missing responses to age of menstruation or prior pregnancies (n=22), were also excluded. Since the focus was on active weightlifters, missing best snatch or clean and jerk in the last 6 months (n=18) were also exclusion criteria. This resulted in an analysis data set of 868 females. Univariate distributions were evaluated numerically and graphically.  DATA-SPECIFIC INFORMATION 1.Number of variables: 51 2.Number of cases/rows: 868 3.Variable List: wlmeno_oa.xlsx 4.Missing data codes: empty cells

opencc-by-4.0May 2023View details →

zenodo44/100

Draft de novo genome assemblies of a male and female Amphibolurus muricatus (jacky dragon)

Four de novo nuclear genome assemblies of Amphibolurus muricatus Assembly 1.0: A 10x Genomics linked-read sequencing assembly • AmpMurF_1.0.fa.tar.gz (female A. muricatus) • AmpMurM_1.0.fa.tar.gz (male A. muricatus) Assembly 1.1: Further scaffolding of assembly 1.0 using RNA-seq data • AmpMurF_1.1.fa.tar.gz (female A. muricatus) • AmpMurM_1.1.fa.tar.gz (male A. muricatus) Assembly 2.0: Further scaffolding of assembly 1.0 using SLR-superscaffolder • AmpMurF_2.0.fa.tar.gz (female A. muricatus) • AmpMurM_2.0.fa.tar.gz (male A. muricatus) Assembly 3.0: An stLFR linked-read sequencing assembly • AmpMurF_3.0.fa.tar.gz (female A. muricatus) • AmpMurM_3.0.fa.tar.gz (male A. muricatus) Methods Assembly 1.0: A 10x Genomics linked-read sequencing assembly Male and female A. muricatus genome sequencing libraries were constructed on the Chromium system (10x Genomics, Pleasanton, CA, USA) by the Ramaciotti Centre for Genomics (Sydney, Australia). The Chromium instrument enables unique barcoding of long stretches of DNA on gel beads. The barcodes allow later reconstruction of long DNA fragments from a series of short DNA fragments with the same barcode (i.e., linked-reads). After barcoding, DNA was sheared into smaller fragments and sequenced on the NovaSeq 6000 platform (Illumina, CA, USA) to generate 151 bp paired-end (PE) reads. A total of 904.9 M raw 10x Genomics Chromium linked-reads were generated. Raw 10x data were assembled with Supernova v2.1.1 (Weisenfeld et al., 2017) and a FASTA file was generated using the ‘pseudohap style’ option in Supernova mkoutput. All female (~450 M) and male (~550 M) read pairs were utilised (female sequencing depth ca 50.3×; male, ca 47.8×). The resulting assemblies was further scaffolded with ARKS v1.0.3 (Coombe et al., 2018), reusing the 10x reads, and the companion LINKS program (v1.8.7) (Warren et al., 2015). ARKS employs a k-mer approach to map linked barcodes to the contigs in the initial Supernova assembly to generate a scaffold graph with estimated distances for LINKS input. These assemblies were denoted AmpMurF_1.0 (female) and AmpMurM_1.0 (male). We used GapCloser v1.12 (part of SOAPdenovo2) (Luo et al., 2012) to fill gaps in the assembly. GapCloser was run using the parameter -l 150) and clean 10x Genomics reads PE reads.   Assembly 1.1: Further scaffolding using RNA-seq data We attempted to improve the v1.0 genome assemblies’ contiguity using RNA-sequencing reads. RNA-seq reads (from brain, ovary, and testis; see below) were filtered (i.e., cleaned) to remove adapters and low-quality reads using Flexbar v3.4.0 and used to further re-scaffold the v1.0 assemblies (FASTA files before gapclosing) with P_RNA_scaffolder (Zhu et al., 2018). The default Flexbar settings discards all reads with any uncalled bases. A final round of scaffolding was performed on the resulting assemblies using L_RNA_scaffolder (Xue et al., 2013). These assemblies were denoted AmpMurF_1.1 (female) and AmpMurM_1.1 (male). As before, GapCloser and clean 10x Genomics reads were used to fill gaps.      Assembly 2.0: Further scaffolding using SLR-superscaffolder As an alternative approach, we attempted to improve the v1.0 genome assemblies’ contiguity using SLR-superscaffolder (Guo et al., 2021). Briefly, SLR-superscaffolder employs single tube long fragment read (stLFR) sequencing (Wang et al., 2019) reads (see section below) to generate hybrid genome assemblies. The software was run with default parameters except for PE_SEED_MIN=300 (minimum contig size to fill; default 1000). These assemblies were denoted AmpMurF_2.0 (female) and AmpMurM_2.0 (male). GapCloser and clean stLFR reads (with the barcode removed using https://github.com/BGI-Qingdao/stLFR_barcode_split) were used to fill gaps.      Assembly 3.0: An stLFR linked-read sequencing and supernova assembly We also generated independent assemblies for the individuals sequenced on the 10x Genomics Chromium system using single tube long fragment read (stLFR) sequencing (Wang et al., 2019). BGI (Brisbane, Australia) generated ~100×-coverage 100-bp paired-end reads (plus a 42-bp stLFR barcode on the right/_2 read). Low-quality reads, PCR duplicates, and adaptors were removed using SOAPnuke v1.5 (Chen et al. 2018). The stLFRdenovo pipeline (<a href="https://github.com/BGI-biotools/stLFRdenovo">https://github.com/BGI-biotools/stLFRdenovo</a>), which is based on Supernova and customized for stLFR data, was used to generate a de novo genome assembly. The stLFRdenovo tool ‘FillGaps’ was used to fill gaps. References Chen, Y., Chen, Y., Shi, C., Huang, Z., Zhang, Y., Li, S., Li, Y., Ye, J., Yu, C., Li, Z., et al. (2018). SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience 7, 1-6. Coombe, L., Zhang, J., Vandervalk, B.P., Chu, J., Jackman, S.D., Birol, I., and Warren, R.L. (2018). ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers. BMC Bioinformatics 19, 234. Guo, L., Xu, M., Wang, W., Gu, S., Zhao, X., Chen, F., Wang, O., Xu, X., Seim, I., Fan, G., et al. (2021). SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme. BMC Bioinformatics 22, 158. Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., et al. (2012). SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1, 18. Wang, O., Chin, R., Cheng, X., Wu, M.K.Y., Mao, Q., Tang, J., Sun, Y., Anderson, E., Lam, H.K., Chen, D., et al. (2019). Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly. Genome Res 29, 798-808. Warren, R.L., Yang, C., Vandervalk, B.P., Behsaz, B., Lagman, A., Jones, S.J., and Birol, I. (2015). LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads. Gigascience 4, 35. Weisenfeld, N.I., Kumar, V., Shah, P., Church, D.M., and Jaffe, D.B. (2017). Direct determination of diploid genome sequences. Genome Res 27, 757-767. Xue, W., Li, J.T., Zhu, Y.P., Hou, G.Y., Kong, X.F., Kuang, Y.Y., and Sun, X.W. (2013). L_RNA_scaffolder: scaffolding genomes with transcripts. BMC Genomics 14, 604. Zhu, B.H., Xiao, J., Xue, W., Xu, G.C., Sun, M.Y., and Li, J.T. (2018). P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads. BMC Genomics 19, 175.

opencc-by-4.0Aug 2023View details →

zenodo44/100

Data from: The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies

The dataset contains intermediate output files required to reproduce the figures in the main text and Supporting Material of Willink et al. 2023. The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies. FILE OVERVIEW: 1. Morph-specific assemblies     A. File names: Afem_1354_ragtag.fasta.gz, Ifem_1049_ragtag.fa.gz, Ofem_0081_ragtag.fa.gz, O054_Shasta_run2.PMDV.HAP1.purged.fasta.gz, A059_Shasta_run1.PMDV.HAP1.purged.fa.gz     B. Description: genome assemblies for different morphs of Ischnura elegans (Afem_1354, Ifem_1049, and Ofem_0081) and Ischnura senegalensis (A059 and O054), generated in this study from long-read Nanopore data using Shasta v 0.7.0 (https://github.com/paoloshasta/shasta). 2. Assembly statistics     A. File names: Assembly_statistics.csv, Assembly_statistics_sen.csv     B. Description: Completeness and quality metrics for de novo genome assemblies of I. elegans and I. senegalensis female morphs. See Fig. S1-S2. 3. Repetitive content annotation     A. File names: A1354_ragtag_RED.bed.repeats.bed.gz, Afem_Shasta1_polished_ragtag_UPPER.fa.out.gz, Ifem_Shasta2_polished_ragtag_UPPER.fa.out.gz, ioIscEleg1.1.primary_UPPER.fa.out.gz, ToL_RED.repeats.bed.gz     B. Description: Annotation of repetitive sequences in morph-specific assemblies. All morph assemblies (A, I and Darwin Tree of Life assemblies) were annotated using RepeatModeler v 2.0.1 and RepeatMasker v 1.0.93 (http://www.repeatmasker.org). The A morph and  DToL assemblies were additionally annotated using Red v 0.0.1 (https://github.com/BioinformaticsToolsmith/Red). RepeatMasker annotations were then used to estimate TE coverage. See Extended Data Fig. 4 and Fig. S7. 4. GWAS output     A. File names: A1354_ragtag_AvI.assoc_filtered.txt.gz, A1354_ragtag_AvO.assoc_filtered.txt.gz, A1354_ragtag_IvO.assoc_filtered.txt.gz, ToL_AvI.assoc_filtered.txt.gz, ToL_AvO.assoc_filtered.txt.gz, ToL_IvO.assoc_filtered.txt.gz     B. Description: filtered SNPs in pairwise association tests between morphs (n = 19 resequencing samples per morph) of I. elegans. Analyses were conducted in PLINK v 1.9 (http://pngu.mgh.harvard.edu/purcell/plink/), using either the A morph assembly (Fig. 2a-b), or the Darwin Tree of Life (DToL) reference assembly (Extended Data Figure 8a-b) as mapping reference. 5. Population statistics     A. File names: Afem_pixy_30K_fst.txt.gz, A1354_30kb.Tajima.D.gz, Afem_pi_30K_pi.txt.gz, ToL_30K_fst.txt.gz, ToL_30kb.Tajima.D.gz, ToL_30K_onepop_pi.txt.gz     B. Description: Genetic differentiation (fst) between morphs, Tajima's D statistics, and nucleotide diversity across 30 kb windows of the I. elegans genome. Population statistics were computed using either the A morph assembly (Fig. 2c-e), or the DToL reference assembly (Extended Data Figure 8c-e) as mapping reference. 6. k-mer based GWAS     A. File names: AvI_kmers.fa.gz, AvO_kmers.fa.gz, OvAI_kmers.fa.gz, AvI_kmers.fa_v_A1354_Shasta_run1_table.tsv.gz, AvO_kmers.fa_v_A1354_Shasta_run1_table.tsv.gz, OvAI_kmers.fa_v_A1354_Shasta_run1_table.tsv.gz, OvAI_kmers.fa_v_Ifem_1049_ragtag_table.tsv.gz     B. Description: List of significant k-mers (in fasta format) in three k-mer based association analyses (n = 19 resequencing samples per morph) between morphs of I. elegans. Significant k-mers were then mapped to morph-specific assemblies using Blast v 2.22.28 (https://blast.ncbi.nlm.nih.gov/Blast.cgi) for short sequences. We include mapping results shown in Fig. 3a-b. 7. Read-depth coverage     A. File names: reseq_coverage_norepeat_500_window.bed.gz, nano_coverage_norepeat_500_window.bed.gz, Ifem_nano_coverage_norepeat_500_window.bed.gz, Ifem_reseq_coverage_norepeat_500_window_15Mb.bed.gz, poolseq_coverage_norepeat_500_window.bed.gz, morph_coverage_norepeat_diff_500.tsv.gz, SwD_popmap     B. Description: Read depth coverage of the morph locus and a 15 mb region used to estimate baseline read depths. 19 Illumina resequencing samples, and one long-read Nanopore sample of each morph of I. elegans were mapped to both the A and I assemblies to estimate read depth. Two poolseq samples (each pool consisting of 30 females of each morph) of I. senegalensis were mapped to the A assembly of I. elegans to estimate read depth. Read depth was estimated in mosdepth v 0.2.8 (https://github.com/brentp/mosdepth) across 500 bp windows after filtering windows with more than 10% repetitive content. For poolseq samples, the difference in coverage values between the A and O pools was computed across the entire genome. Sample information for resequencing samples is recorded in the file SwD_popmap. See Fig. 3c-d, 5b, and S8. 8. Assembly alignment     A. File names: nucmer_aln_Ifem_1049_ragtag_Afem_1354_ragtag.qr1_filter.reformat.coords.gz, nucmer_aln_Ofem_0081_ragtag_Afem_1354_ragtag.qr1_filter.reformat.coords.gz, nucmer_aln_Afem_Isen_Afem_Iele.qr1_filter.reformat.coords.gz, nucmer_aln_Ofem_Isen_Afem_Iele.qr1_filter.reformat.coords.gz, karyotype_AI_RagTag.csv, karyotype_AO_RagTag.csv, karyotype_AIsen_AIele.cs, karyotype_OIsen_AIele.csv     B. Description: Assembly alignments using nucmer v 4.0.0 (https://github.com/mummer4/mummer) and contig synteny for plotting using RIdeogram v 0.2.2 (https://cran.r-project.org/web/packages/RIdeogram/vignettes/RIdeogram.html) in R v 4.2.2 (https://www.r-project.org/). The A morph assembly of I. elegans was aligned to the I and O morph assemblies of I. elegans and to the A and O-like assemblies of I. senegalensis. See Fig. 4a, 5c. 9. Genotyping the Darwin Tree of Life assembly     A. File names: nucmer_aln_Afem_ragtag_ToL-haplotigs.qr1_filter.reformat.coords.gz, nucmer_aln_Afem_ragtag_ToL-primary.qr1_filter.reformat.coords.gz, ToL_500_norepeat.regions.bed.gz, karyotype_AToL_13_unloc_RagTag.csv, karyotype_AToL_RagTag_haplotigs.csv     B. Description: To genotype the DToL reference assembly of I. elegans, we estimated read-depth coverage of the DToL long-read Pacbio data mapped to the A morph assembly of I. elegans generated in this study, and aligned the A morph assembly to both the primary DToL assembly and to the purged haplotigs. Read depth was estimated in mosdepth v 0.2.8 (https://github.com/brentp/mosdepth) and assembly alignments were conducted using nucmer v 4.0.0 (https://github.com/mummer4/mummer). See Fig. S3. 10. SV calling     A. File names: A_to_A.bam, A_to_A.bam.bai, A_to_I.bam, A_to_I.bam.bai, A_to_O.bam, A_to_O.bam.bai, A_to_ToL_2mb.bam, A_to_ToL_2mb.bam.bai, I_to_A.bam, I_to_A.bam.bai, I_to_I.bam, I_to_I.bam.bai, I_to_O.bam, I_to_O.bam.bai, I_to_ToL_2mb.bam, I_to_ToL_2mb.bam.bai, O_to_A.bam, O_to_A.bam.bai, O_to_I.bam, O_to_I.bam.bai, O_to_O.bam, O_to_O.bam.bai, O_to_ToL_2mb.bam, O_to_ToL_2mb.bam.bai     B. Description: mergede alignements of resequencing samples (n = 19 per morph) to alternative reference assemblies (A, I, O, and DToL) for I. elegans. The alignments have been filtered by quality and to contain only the unlocalized scaffold 2 of chromosome 13, which includes the morph locus. These files were used to call morph-specific structural variants using samplot v 1.3.0 (https://github.com/ryanlayer/samplot). See Extended Data Figs 2, 7, and Fig. S5-S6. 11. Mapping of inversion breakpoint reads     A. File names: AvO_3K.tsv.gz, AvO_22K.tsv.gz, AvO_sen_3K.tsv.gz, AvO_sen_22K.tsv.gz, IvO_3K.tsv.gz     B. Description: Signatures of an inversion with breakpoints at ~ 3 kb and ~ 22 kb of the unlocalized scaffold 2 of chromosome 13 on the O assembly were found in A and I resequencing samples of I. elegans and in poolseq samples of A females of I. senegalensis. We queried the reads mapping to the inversion breakpoints and then tabulated their mapping locations of the A morph assembly of I. elegans (Fig. 6 and Extended Data Fig. 3, 7b-c). For the first inversion breakpoint, we also mapped reads on the I morph assembly of I. elegans (Fig. S12). 12. Evidence of translocation in I     A. File names: Ifem_nano_SUPER_13_unloc_2.bam, Ifem_nano_SUPER_13_unloc_2.bam.bai     B. Description: Long-read Nanopore data of a I morph female of I. elegans mapped to the A morph of I. elegans and filtered to contain the entire unlocalized scaffold 2 of chromosome 13. Read mapping was conducted in minimap2 v 2.22-r1110 (https://github.com/lh3/minimap2) and used to identify a translocation signature in the I morph, relative to the A morph of I. elegans. See Extended Data Fig. 6. 13. PCA output     A. File names: A1354_all.eigenval, A1354_all.eigenvec, I1049_all.eigenval, I1049_all.eigenvec     B. Description: Eigenvectors and eigenvalues of PCA analyses of population structure between morphs of I. elegans. PCA analysis were conducted on morph locus, using either the A morph or the I morph assembly as mapping reference in PLINK v 1.9 (http://pngu.mgh.harvard.edu/purcell/plink/). See Fig. S4. 14. Linkage disequilibrium     A. File names: A1354_SUPER_1_allr.ld.gz, A1354_SUPER_2_allr.ld.gz, A1354_SUPER_3_allr.ld.gz, A1354_SUPER_4_allr.ld.gz, A1354_SUPER_5_allr.ld.gz, A1354_SUPER_6_allr.ld.gz, A1354_SUPER_7_allr.ld.gz, A1354_SUPER_8_allr.ld.gz, A1354_SUPER_9_allr.ld.gz, A1354_SUPER_10_allr.ld.gz, A1354_SUPER_11_allr.ld.gz, A1354_SUPER_12_allr.ld.gz, A1354_SUPER_13_allr.ld.gz, A1354_SUPER_13_unloc_1_allr.ld.gz, A1354_SUPER_13_unloc_2_allr.ld.gz, A1354_SUPER_13_unloc_3_allr.ld.gz, A1354_SUPER_13_unloc_4_allr.ld.gz, A1354_SUPER_X_allr.ld.gz     B. Description: Estimates of recombination rate (R2) between SNPs across the first 15 mb of each chromosome and unlocalized segments of chromosome 13 of I. elegans. Recombination rates were estimated based on 57 resequencing samples and using the A morph assembly as mapping reference in PLINK v 1.9 (http://pngu.mgh.harvard.edu/purcell/plink/). See Extended Data Fig. 5. 15. Gene annotations     A. File names: Afem_all_ragtag.gtf.gz, Afem_all_transcripts.transdecoder.genome.gff3.gz, Isen.gtf.gz     B. Description: Annotation of the A morph assembly of I. elegans using RNAseq data to assemble transcripts de novo for I. elengans and I. senegalensis in Stringtie v 2.1.4 (https://ccb.jhu.edu/software/stringtie/). Peptide sequences for the I. elegans transcripts were then predicted using Transdecoder v 5.5.0 (https://github.com/TransDecoder/TransDecoder). 16. Gene annotations in the morph locus     A. File names: gene_models_shared_trancripts_simple.csv, gene_models_shared_trancripts_simple_I.csv     B. Description: locations of exon features for genes in the morphs locus and expressed in at least one adult sample of both I. elegans and I. senegalensis. Locations are given for the A and I assemblies. See Fig. 6 and S12. 17. Gene expression     A. File names: DToL_gene_count_matrix.csv.gz, DToL_transcript_count_matrix.csv.gz, gene_count_matrix.csv.gz, transcript_count_matrix.csv.gz, Isen_gene_count_matrix.csv.gz, Isen_transcript_count_matrix.csv.gz, Iele_phenodata.csv, Isen_phenodata.csv     B. Description: Sample information (phenodata), gene and transcript count matrices for gene expression analysis. For I. elegans, gene expression was quantified on thoracic tissue of six adult females of each morph and six adult males (three sexually mature and three sexually immature in each group). Reads were mapped to both the A morph assembly and the DToL reference assembly. For I. senegalensis, we used previously published data (NCBI BioProject PRJDB11387) from different tissues of adult females of each morph and males (one upon emergence and one two days after emergence for each group) mapped to the A morph assembly. Gene and transcript counts were generated using Stringtie v 2.1.4 (https://ccb.jhu.edu/software/stringtie/). See Fig. 6, S9-S11, S13. 18. SNPs in the morph locus     A. File names: A1354-ragtag-allsites-candidate_gene_cds.vcf.gz, A1354-ragtag-allsites-candidate_gene_cds.vcf.gz.tbi, vcf_popmap     B. Description: SNPs in 57 resequencing samples across coding sequences of the morph locus of I. elegans. The A morph assembly was used as mapping reference. Sample information for resequencing samples is recorded in the file vcf_popmap. See Fig. S14a. 19. Domains and orthologues of Gastrula zinc-finger transcription factor in the morph locus     A. File names: GZnf_domain_annot.csv, GZnF_orthologue.tre, GZnf_orthologue_annot.txt     B. Description: Functional domains were annotated using InterProScan (https://www.ebi.ac.uk/interpro/). The gene orthologue tree was inferred using OrthoFinder v 2.5.2 (https://github.com/davidemms/OrthoFinder). See Fig. S14.

opencc-by-4.0Sep 2023View details →

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Female mouse 60d water uranium exposure

Female mice were exposed to uranium in the drinking water for 60 days. Doses of uranium (in the form of uranyl acetate) were 0, 5, and 50 ppb. We examined 1) immune function of splenocytes (mitogenesis) 2) lymphocyte population subsets in the bone marrow, spleen and thymus (flow cytometry) 3) erythroid cell differentiation in the bone marrow (flow cytometry) 4) uranium concentrations in kidney, femur bone, liver, blood spleen thymus and bone marrow (ICP-MS).

openCC (other)Apr 2020View details →

zenodo40/100

Figs. 15-17. Female genitalia. 15 in Two new species of the genus Chloropepla (Hemiptera: Pentatomidae: Pentatominae) from Brazil*)

Figs. 15-17. Female genitalia. 15 – Chloropepla paveli sp. nov., genital plates. 16-17 – C. stysi sp. nov., female genitalia. 16 – genital plates; 17 – gonocoxites and gonapophyses of ninth segment and ectodermal genital ducts. Scale bars = 1 mm (aac – anterior annular crest; cs – capsula seminalis; ch – chitinellipsen; g9 – gonapophyses 9; gc8 – gonocoxites 8; gc9 – gonocoxites 9; la8 – laterotergites 8; la9 – laterotergites 9; pac – posterior annular crest; pco – pars communis; pi – pars intermedialis; tvi – thickening of vaginal intima; X – segment X).

opencc-by-4.0Dec 2008View details →

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Figure 8. Female genital plates and ectodermal genital ducts. A in Revision of Cataulax Spinola, with Architas Distant as a New Synonymy (Heteroptera: Pentatomidae: Discocephalini)

Figure 8. Female genital plates and ectodermal genital ducts. A) C. eximius Stål, 1860; B) C. pudens (Distant, 1889); C) C. subtiliterconspersus, n. sp. (aac = anterior anular crest, ch = chitinellipsen, cs = capsula seminalis, dr = ductus receptaculi, g9 = gonapophyses 9, gc9 = gonoxites 9, la9 = laterotergites 9, or = orificium receptaculi, pac = posterior anular crest, pi = pars intermedialis, tvi = thickening of vaginal intima, X = 10th abdominal segment ) .

opencc-by-4.0Sep 2000View details →

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Figs. 62–67. Female genital plates, ventral view. 62 in Review of Thoreyella Spinola with the description of two new species from Brazil (Heteroptera, Pentatomidae)

Figs. 62–67. Female genital plates, ventral view. 62, Thoreyella paraiba sp. nov; 63, T. cornuta; 64, T. taurus; 65, T. maracaja sp. nov.; 66, T. brasiliensis; 67, T. trinotata. gc8, gonocoxites 8; g8, gonapophyses 8; la8, laterotergites 8; la9, laterotergites 9; s, spiracle; VII, seventh abdominal segment; X, tenth segment. Scale = 1 mm.

opencc-by-4.0Sep 2011View details →

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Dataset from "Collection of kinematic and kinetic data of young & adult, male & female subjects performing periodic and transient gait tasks for gait pattern recognition"

Written by: Paolo Mistretta Contact information: paolo.mistretta@phd.unipd.it Date: 24/01/2020 This document contains supplementary material for the article “Collection of kinematic and kinetic data of young & adult, male & female subjects performing periodic and transient gait tasks for gait pattern recognition” (Authors: Paolo Mistretta, Cecilia Marchesini, Andrea Volpini, Luca Tagliapietra, Tommaso Sciarra, Aldo Lazich, Salvatore Forte, Mauro De Matteis, Emanuele Menegatti and Nicola Petrone) presented at the 13th conference of the International Sports Engineering Association, Tokyo, Japan, 22-25 June 2020. Data are contained in the file: “database_ISEA2020.mat”

opencc-by-4.0Jan 2020View details →

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Figures 36–41. Eupogonius giesberti, holotype female. 36 in A new genus, a new species, new combinations, and notes on synonymy and nomenclature in American Desmiphorini (Coleoptera, Cerambycidae, Lamiinae)

Figures 36–41. Eupogonius giesberti, holotype female. 36) Dorsal view. 37) Ventral view. 38) Lateral view. 39) Head, frontal view. 40) Right eye. 41) Mesotibia.

opencc-by-4.0Jan 2018View details →

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Figures 13–15. Caraphia warneri, holotype female. 13 in A synopsis of American Caraphia Gahan, 1906 (Coleoptera: Cerambycidae: Lepturinae) with description of two new species

Figures 13–15. Caraphia warneri, holotype female. 13) Dorsal habitus. 14) Ventral habitus. 15) Lateral habitus.

opencc-by-4.0Dec 2018View details →

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Figs 1–11. Female tarsomeres I in Some techniques for the study of useful characters in the taxonomy of the genus Timarcha Samouelle, 1819 (Coleoptera, Chrysomelidae)

Figs 1–11. Female tarsomeres I–III in ventral view. 1. Timarcha maroccana (Morocco, Azerzou). 2. T. scabripennis (Morocco, Souk-el-Khemis des Anjra). 3. T. prujai (Morocco, Bab Berret). 4. T. balearica (Spain, Mallorca). 5. T. tenebricosa (France, Bretagne, Morlaix). 6. T. nicaeensis (Italy, Alpi Liguri, Margheria dei Boschi). 7. T. lusitanica (Portugal, Oeiras). 8. T. goettingensis (France, Versailles). 9. T. intermedia (Spain, Granada, Motril). 10. T. pimelioides (Italy, Sicily, Portella Misilbesi). 11. T. rugosa (Algeria, Biskra). Abbreviations: a = protarsomeres; b = mesotarsomeres; c = metatarsomeres. Scale bar = 2.0 mm.

opencc-by-4.0Apr 2020View details →

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Figure 22. Zehntnerobolus rubripes comb. n., A, C–G male lectotype, B female paratype, A telson B, C right midbody leg D anterior gonopod, anterior view E anterior gonopod, posterior view F left posterior gonopod, anterior view G in Review of the Spirobolida on Madagascar, with descriptions of twelve new genera, including three genera of 'fire millipedes' (Diplopoda)

Figure 22. Zehntnerobolus rubripes comb. n., A, C–G male lectotype, B female paratype, A telson B, C right midbody leg D anterior gonopod, anterior view E anterior gonopod, posterior view F left posterior gonopod, anterior view G left posterior gonopod, posterior view. Apo = apodeme; av = anal valves; Cx = coxite; Gr = groove; Pre = preanal ring; St = sternite; sub = subanal scale; T = telopodite; Tp = telopodite process. Scale bars = 1 mm.

opencc-by-4.0Sep 2009View details →

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Figure 4. Odontoxenus thailandicus. A elytron B pronotum C male abdominal tergite VIII D male abdominal sternite VIII E male abdominal tergite IV & V F female abdominal tergite VIII G in Two new species of Aleocharinae (Coleoptera, Staphylinidae) found in fungus gardens of Odontotermes termites (Isoptera, Termitidae, Macrotermitinae) in Khao Yai National Park, Thailand

Figure 4. Odontoxenus thailandicus. A elytron B pronotum C male abdominal tergite VIII D male abdominal sternite VIII E male abdominal tergite IV & V F female abdominal tergite VIII G median lobe of aedeagus, and H spermatheca.

opencc-by-4.0Jun 2010View details →

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Fig. 8. Female genitalia. A in Description of Sharon gen. nov. for the Chilean species Asaphes amoenus Philippi, 1861 (Coleoptera: Elateridae)

Fig. 8. Female genitalia. A. Sharon amoenus (Philippi, 1861) comb. nov. B. Hemicrepidius memnonius Herbst, 1806. Scale bars = 0.5 mm.

opencc-by-3.0Oct 2015View details →

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Fig. 7. Begonia acetosella Craib. A. Plant habit. B – C. Leaf variation. D. Female bud. E. Female flower. F in A revision and one new species of Begonia L. (Begoniaceae, Cucurbitales) in Northeast India

Fig. 7. Begonia acetosella Craib. A. Plant habit. B – C. Leaf variation. D. Female bud. E. Female flower. F. Reverse of flower. G. Styles. Photographs by Rebecca Camfield of a plant in cultivation at the Royal Botanic Garden Edinburgh (accession 19980065).

opencc-by-4.0Jan 2018View details →

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Figures 1-8 in A description of the flea species Paractenopsyllus madagascarensis n. sp. and the female sex of Paractenopsyllus raxworthyi Duchemin & Ratovonjato, 2004 (Siphonaptera, Leptopsyllidae) from Madagascar with a key to the species of Paractenopsyllus

Figures 1-8. Paractenopsyllus madagascarensis sp. n. 1 Head and thorax, holotype 3 (SMG-13919). 2 Head and thorax, allotype ♀ (SMG-13903). 3 Aedeagus, paratype 3 (SMG-14002). 4 Apex of aedeagus, paratype 3 (SMG-14002). 5 Basimere and telomere, mesal aspect, paratype 3 (SMG-14002). 6 Eighth tergite, paratype 3, (SMG-14002). 7 Eighth sternite, paratype 3 (SMG-14002). 8 Ninth sternite, paratype 3 (SMG-14002). Scale = 200µ

opencc-by-4.0Jul 2009View details →

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Figure 14-16 in A description of the flea species Paractenopsyllus madagascarensis n. sp. and the female sex of Paractenopsyllus raxworthyi Duchemin & Ratovonjato, 2004 (Siphonaptera, Leptopsyllidae) from Madagascar with a key to the species of Paractenopsyllus

Figure 14-16. Paractenopsyllus raxworthyi, ♀ (MR-172). 14 Head and pronotum. 15 Seventh sternum and eighth tergum. 16 Spermatheca and bursa copulatrix. Scale 14-15 = 200µ, 16 = 100µ

opencc-by-4.0Jul 2009View details →

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Figure 9-13 in A description of the flea species Paractenopsyllus madagascarensis n. sp. and the female sex of Paractenopsyllus raxworthyi Duchemin & Ratovonjato, 2004 (Siphonaptera, Leptopsyllidae) from Madagascar with a key to the species of Paractenopsyllus

Figure 9-13. Paractenopsyllus madagascarensis sp. n. 9 Seventh sternite and terminalia, allotype ♀ (SMG- 13903). 10 Spermatheca and bursa copulatrix, allotype ♀ (SMG-13903). 11 Spermatheca and bursa copulatrix, paratype ♀ (SMG-13935). 12 Anal stylet, paratype ♀ (SMG-13918). 13 Hind tibia, holotype 3 (SMG-13919). Scale 9 and 13 = 200µ, 10-12 = 100µ

opencc-by-4.0Jul 2009View details →

ScienceDex guides

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Allen Brain Atlas

Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.

allen-brain-atlas

neuroscienceopenDocumentation, web resources, and API references are available online.

Last verified 2026-04-30Open record

Annotated Behaviour and Observability Dataset (ABODe)

ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.

abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

DANDI Archive for NWB datasets

DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

International Brain Laboratory public data

The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

OpenNeuro

OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record