Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
34
datasets available to search
ShareScore release 0.9.0
Dataset results
34 results for “Acomys”
De novo transcriptome assemblies for the spiny mouse (Acomys cahirinus)
<p>Transcriptome assemblies generated per https://dx.doi.org/10.1101/076067 (preprint) / https://dx.doi.org/10.17504/protocols.io.ghebt3e (protocol). Manuscript available at Scientific Reports.</p>
Figure 3 in Distribution and conservation of Acomys cilicicus (Mammalia: Rodentia) in Turkey
Figure 3. IUCN distribution map of Acomys cilicicus (yellow dashed area). Blue dashed areas (1 to 7 on map) show destroyed/changed habitats between 2004 and 2017.
Figure 2 in Distribution and conservation of Acomys cilicicus (Mammalia: Rodentia) in Turkey
Figure 2. The distribution and relative abundance of Acomys cilicicus and Apodemus mystacinus samples in study area.
Figure 5 in Distribution and conservation of Acomys cilicicus (Mammalia: Rodentia) in Turkey
Figure 5. Habitat change in the distribution area of Acomys cilicicus. Blue and green dashed areas (4–7 on map) show destroyed/changed habitats between 2004 and 2017.
Figure 1 in Distribution and conservation of Acomys cilicicus (Mammalia: Rodentia) in Turkey
Figure 1. Sampling localities. The numbers of localities are the same as in Table 1. Blue circles indicate trapping localities where no Acomys cilicicus samples were collected and red circles indicate the localities where Acomys cilicicus samples were collected. Green dashed areas show the estimated distribution areas of two isolated populations (A and B on map) of Acomys in the study area, and yellow dashed area (C on map) shows the IUCN distribution map of Acomys cilicicus.
Figure 4 in Distribution and conservation of Acomys cilicicus (Mammalia: Rodentia) in Turkey
Figure 4. Habitat change in the distribution area of Acomys cilicicus. Blue and green dashed areas (1, 2, 3, and 7 on map) show destroyed/ changed habitats between 2004 and 2017.
Figure 4. Small mammals recorded from Farasan Archipelago. A. Rhinopoma cystops. B. Asellia patrizii. C. Pipistrellus kuhlii. D. Acomys dimidiatus E. Rattus rattus. F in Small mammals from Farasan Archipelago, Saudi Arabia
Figure 4. Small mammals recorded from Farasan Archipelago. A. Rhinopoma cystops. B. Asellia patrizii. C. Pipistrellus kuhlii. D. Acomys dimidiatus E. Rattus rattus. F. Gerbillus nanus.
Additional annotation, alignment, and results from Ka/Ks analysis for Chromosomal-level reference genome assembly of the African Spiny Mouse (Acomys cahirinus)
<p><strong>Annotation files, alignments, and results summaries from Chromosomal-level reference genome assembly of the African Spiny Mouse (Acomys cahirinus).</strong></p> <p>Pairwise genome alignments contain the .maf suffix</p> <p>FASTA alignments from stitched gene blocks contain the .fasta suffix</p> <p>CSV file containing the Ka/Ks results</p> <p>RepeatMasker .out file</p>
Figure 6 in Reproductive biology of Acomys cilicicus Spitzenberger, 1978 (Rodentia: Muridae) in Turkey
Figure 6. Suckling process.
Figure 1 in Reproductive biology of Acomys cilicicus Spitzenberger, 1978 (Rodentia: Muridae) in Turkey
Figure 1. Picture of the amniotic membrane stuck to the face and shoulder area.
Figure 4 in Reproductive biology of Acomys cilicicus Spitzenberger, 1978 (Rodentia: Muridae) in Turkey
Figure 4. Molars on the mandible of a newborn offspring.
Figure 3 in Reproductive biology of Acomys cilicicus Spitzenberger, 1978 (Rodentia: Muridae) in Turkey
Figure 3. Mother and newborn offspring after birth.
Chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus)
<p>Genomic DNA was extracted from blood from a single male A. cahirinus animal using a Monarch HMW DNA Extraction Kit for Cells & Blood (T3050, New England Biolabs, Ipswich MA) following the manufacturer’s recommended protocol. DNA was quantified prior to library construction using the Qubit DNA HS Assay (ThermoFischer, Waltham MA) and DNA fragment lengths were assessed using the Agilent Femto Pulse System (Santa Clara, CA). Libraries were prepared for sequencing using the Oxford Nanopore ligation kit (SQK-LSK110) following the manufacturers’ instructions, except that DNA repair and A-tailing was performed for 30 min and the ligation was allowed to continue for 1 hr. Prepared libraries were quantified using a Qubit fluorometer and 30 fmol of the library was loaded onto a Nanopore version R.9.4.1 flow cell and loaded on a PromethION running MinKNOW version (21.05.20). To increase output, the flow cell was washed after approximately 24 hr of sequencing then an additional 12 fmol of library was added to the flow cell and run for an additional 48 hr. Basecalling was performed using Guppy 5.0.12 (Oxford Nanopore) using the superior model (dna_r9.4.1_450bps_sup_prom.cfg). FASTQ files for assembly were extracted from unaligned bam files using samtools (Li et al. 2009) then Flye version 2.9 for assembly using the --nano-hq flag (Kolmogorov et al. 2019). Haplotigs and overlaps in the assembly were purged using purge_dups (https://github.com/dfguan/purge_dups). The assembly was then polished using Medaka version 1.4.2 (https://github.com/nanoporetech/medaka) followed by a second polishing step with pilon version 1.24 (Walker et al. 2014). Assembly statistics at each step were generated using Quast (Gurevich et al. 2013) and BUSCO (Simão et al. 2015) (Table S2). The primary contigs assembled from the Nanopore data were anchored to chromosomes using 505,210,505 read pairs of a Hi-C library isolated from another A. cahirinus individual of unknown sex downloaded from the NCBI Short Read Archive (SRX13258644) (Wang et al. 2022). After aligning the Hi-C reads with the ArimaHi-C Mapping Pipeline (https://github.com/ArimaGenomics/mapping_pipeline), YaHS v1.0 (Zhou et al. 2023) was used with default error correction for scaffolding, and Juicebox v1.11.08 (Dudchenko et al. 2018) was used to generate a Hi-C contact map. Progressive Cactus was used (Armstrong et al. 2020) to perform a whole-genome alignment of the A. cahirinus draft assembly to the Mus musculus GRCm39 reference genome (RefSeq GCF_000001635.27_GRCm39). Comparative annotation of the draft genomes was then performed using the Comparative Annotation Toolkit (CAT) (Fiddes et al. 2018). Briefly, the M. musculus RefSeq annotation GFF was parsed and validated with the “parse_ncbi_gff3” and “validate_gff3” programs (respectively) from CAT. The M. musculus reference transcript cDNA sequences were downloaded and mapped to the M. musculus draft genome with minimap2 (Li 2018) and provided to CAT as long-read RNA-seq reads in the “[ISO_SEQ_BAM]” field of the configuration file. For A. cahirinus, bulk RNA-seq data obtained from multiple pooled organs were downloaded from NCBI SRA BioProject PRJNA342864 (Bellofiore et al. 2017) and mapped to the draft assembly with STAR (Dobin et al. 2013) then provided to CAT in the “[BAMS]” field. CpG islands were identified using the cpg_lh utility from the UCSC suite of tools (Kent et al. 2002).</p>
On following pages: 4. Golden Spiny Mouse (Acomys russatus); 5. Arabian Spiny Mouse (Acomys dimidiatus); 6. Seurat's Spiny Mouse (Acomys seurati); 7. Northeast African Spiny Mouse (Acomys cahirinus); 8. Louise's Spiny Mouse (Acomys louisae); 9. Mullah Spiny Mouse (Acomys mullah); 10. Chudeau''s Spiny Mouse (Acomys chudeaui); 11. John's Spiny Mouse (Acomys johannis); 12. Gray Spiny Mouse (Acomys cineraceus); 13. Percival's Spiny Mouse (Acomys percivali); 14. Wilson's Spiny Mouse (Acomys wilsoni); 15. Kemp's Spiny Mouse (Acomys kempi); 16. Fiery Spiny Mouse (Acomys ignitus); 17. Muze Spiny Mouse (Acomys muzel); 18. Nguru Spiny Mouse (Acomys ngurui); 19. Southern African Spiny Mouse (Acomys spinosissimus); 20. Selous's Spiny Mouse (Acomys selousi); 21. Cape Spiny Mouse (Acomys subspinosus); 22. Congo Forest Rat (Deomys ferrugineus). in Muridae
On following pages: 4. Golden Spiny Mouse (Acomys russatus); 5. Arabian Spiny Mouse (Acomys dimidiatus); 6. Seurat's Spiny Mouse (Acomys seurati); 7. Northeast African Spiny Mouse (Acomys cahirinus); 8. Louise's Spiny Mouse (Acomys louisae); 9. Mullah Spiny Mouse (Acomys mullah); 10. Chudeau''s Spiny Mouse (Acomys chudeaui); 11. John's Spiny Mouse (Acomys johannis); 12. Gray Spiny Mouse (Acomys cineraceus); 13. Percival's Spiny Mouse (Acomys percivali); 14. Wilson's Spiny Mouse (Acomys wilsoni); 15. Kemp's Spiny Mouse (Acomys kempi); 16. Fiery Spiny Mouse (Acomys ignitus); 17. Muze Spiny Mouse (Acomys muzel); 18. Nguru Spiny Mouse (Acomys ngurui); 19. Southern African Spiny Mouse (Acomys spinosissimus); 20. Selous's Spiny Mouse (Acomys selousi); 21. Cape Spiny Mouse (Acomys subspinosus); 22. Congo Forest Rat (Deomys ferrugineus).
FIGURE 9 in Contribution to the systematics and zoogeography of the East-African Acomys spinosissimus Peters 1852 species complex and the description of two new species (Rodentia: Muridae)
FIGURE 9. (A) Type specimens of Acomys ngurui (top) and Acomys muzei (bottom). (B) Dorsal and ventral view of the skulls of the type specimen of Acomys ngurui (left) and Acomys muzei (right).
FIGURE 7 in Contribution to the systematics and zoogeography of the East-African Acomys spinosissimus Peters 1852 species complex and the description of two new species (Rodentia: Muridae)
FIGURE 7. (A) Combined canonical analysis of the OTU's that cover most of the geographic range of the A. spinosissimus species complex. (B) Morphometric UPGMA tree diagram of all the studied OTU's based on the square root of the Mahalanobis squared distances. Type specimens of A. selousi and A. spinosissimus are represented by OTU60 and OTU50, we labeled them accordingly.
FIGURE 6 in Contribution to the systematics and zoogeography of the East-African Acomys spinosissimus Peters 1852 species complex and the description of two new species (Rodentia: Muridae)
FIGURE 6. (A) Canonical analysis of the southern African Acomys OTU 40, 50 and 60 (on which the type of selousi is plotted). (B) The same canonical analysis with a reduced set of measurements allowed plotting the damaged skull of the A. spinosissimus lectotype.
FIGURE 4 in Contribution to the systematics and zoogeography of the East-African Acomys spinosissimus Peters 1852 species complex and the description of two new species (Rodentia: Muridae)
FIGURE 4. Bayesian tree based on complete cyt b sequences for all A. spinossisimus populations with corresponding OTU numbers and clade assignations. Species names are preceded by EMBL accession numbers for already published sequences, number preceding a locality name is the museum or specimen number. Support values above the nodes of this phylogeny indicate the degree of support provided by Bayesian analysis, below by ML. Sequenced type specimens are indicated with an asterisk.
FIGURE 5 in Contribution to the systematics and zoogeography of the East-African Acomys spinosissimus Peters 1852 species complex and the description of two new species (Rodentia: Muridae)
FIGURE 5. UPGMA tree derived from Wright's (1978) Prevosti distances for Tanzanian Acomys populations calculated from 14 enzyme-loci.
FIGURE 2 in Contribution to the systematics and zoogeography of the East-African Acomys spinosissimus Peters 1852 species complex and the description of two new species (Rodentia: Muridae)
FIGURE 2. The tooth-wear classes distinguished in Tanzanian A. spinosissimus. Cl. 1: all teeth fully erupted; wear minimal; M1 and M2: dentine of 2nd cusp-row not continuous. (RMCA 96.036-M-4828), Cl. 2: light wear; M1 and M2: dentine of the 2nd cusp-row continuous, but width of dentine-surface of t5, enamel-rim of t5. (RMCA 96.036-M-4742), Cl. 3: wear obvious but not extensive; M1: dentine-surface of t5> than enamel-rim of t5; M2: dentine-surface of 1st and 2nd row not continuous. (RMCA96.036-M-4794), Cl. 4: wear extensive; M1: much flattened cusps but still 3 separate dentine-rows; M2: 1st and 2nd dentine-rows communicating. (RMCA 96.036-M-4792), Cl. 5: wear severe; M1: very heavily eroded and at least two dentinerows continuous; M2: continuous dentine wear surface. (RMCA 96.036-M-4856).
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.
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.
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.
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.
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.