cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102196
title: Supporting data for "Living in darkness: Exploring adaptation of <i>Proteus anguinus</i> in 3D by X-ray imaging"

description: The lightless caves can harbour a wide range of living organisms. Cave animals have evolved a set of morphological, physiological and behavioural adaptations known as troglomorphisms, enabling their survival in perpetual darkness, narrow temperature and humidity ranges, and nutrient scarcity of subterranean environment. In this study, we focused on adaptations of skull shape and sensory systems in blind cave salamander, <i>Proteus anguinus</i>, also known as olm or simply proteus - the largest cave tetrapod and the only European amphibian living exclusively in subterranean environments. This extraordinary amphibian compensates the loss of sight by enhanced non-visual sensory systems including mechanoreceptors, electroreceptors and chemoreceptors. We compared developmental stages of <i>Proteus anguinus</i> with <i>Ambystoma mexicanum</i>, also known as axolotl, to make an exemplary comparison between cave-and surface-dwelling paedomorphic salamanders. <br>We used contrast-enhanced X-ray computed microtomography for the 3D segmentation of the soft tissues in the head of <i>Proteus anguinus</i> and axolotl. Sensory organs were visualised to understand how the animal is adapted to living in complete darkness. X-ray microCT datasets were provided along with with 3D models for larval, juvenile and adult specimens, showing the cartilage of the chondrocranium, the position, shape and size of the brain, eyes and olfactory epithelium. <br><i>Proteus anguinus</i> still keeps some of its secrets to itself. Our high-resolution X-ray microCT scans together with 3D models of the anatomical structures in the head may help us to understand the nature and origin of the mechanisms behind its adaptations to the subterranean environment, which led to a series of troglomorphies.
DOI: 10.5524/102157
title: Genome data of the bird of paradise, Astrapia rothschildi

description: The Astrapia rothschildi, common name Huon astrapia, is a medium-size bird-of-paradise measuring approximately 69 cm long. The male has black plumage with a glossy blue crown, dark olive-green back, an iridescent purple-green elongated nape feathers, and a very long and broad purplish black tail. The female is smaller than male, and has blackish-brown plumage with pale barring on its abdomen. It is distributed and endemic to the mountain forests of Huon Peninsula, Papua New Guinea where its diet consists mainly of fruits and seeds (Wikipedia). <br> Here we present the de novo assembled genome totalling 1.03Gb in length, with 2081 scaffolds having an N50 of 7.7Mb, annotated with 16260 coding genes and BUSCO analysis demonstrating a 95% completeness.
DOI: 10.5524/102158
title: Genome data of the bird of paradise, Lycocorax pyrrhopterus

description: The Lycocorax pyrrhopterus, common name, paradise-crow or silky crow, is a medium-sized crow-like bird-of-paradise. One of the few monogamous birds-of-paradise, the paradise-crow is endemic to lowland forests of North Maluku in Indonesia. The diet consists mainly of fruits and arthropods. The paradise-crow is approximately 34 cm long with all-dark, soft and silky plumage. It has a black bill, crimson eyes, and a call reminiscent of a dog's bark. Both sexes are similar; the female is slightly smaller than the male. The breeding season is approximately December to June, (Wikipedia).<br>Here we present the de novo assembled genome totalling 1.07Gb in length, with 3216 scaffolds having an N50 of 4.2Mb, annotated with 17,023 protein coding genes and BUSCO analysis demonstrating a 93.8% completeness.
DOI: 10.5524/102159
title: Genome data of the bird of paradise, Ptiloris paradiseus

description: The Ptiloris paradiseus, common name paradise riflebird, is a bird-of-paradise species endemic to eastern Australia, where it occurs in the rainforests of New South Wales and central Queensland. The paradise riflebird is medium-sized, up to 30 cm long. The male is black with an iridescent greenish blue crown, throat and central tail feathers. It has a black curved bill, black feet, dark brown iris and yellow mouth. The female is an olive brown bird with barred blackish below with a long white brow above her eye. The diet consists mainly of insects and fruits. In displays, the male extends his wings and fans them upward with its head behind the wings to expose his metallic green throat feathers. He then moves his head from side to side with open bill to show off his bright yellow mouth.(Wikipedia).<br>Here we present the de novo assembled genome totalling 1.04Gb in length, with 2062 scaffolds having an N50 of 4.27Mb, annotated with 17,269 protein coding genes and BUSCO analysis demonstrating a 95.1% completeness. This genome assembly was used as the reference genome for alignment of the Paradisaea rubra and Pteridophora alberti reads generated from museum tissue.
DOI: 10.5524/102175
title: Genomic data from Galápagos penguin (<em>Spheniscus mendiculus</em>).

description: The Galápagos penguin is endemic to the Galápagos Islands, and is the only penguin with breeding colonies north of the equator. The cool waters of the Humboldt and Cromwell Currents allow the species to survive in the tropics, and they have evolved unique adaptations to survive in a tropical environment. The International Union for Conservation of Nature (IUCN) classifies them as endangered.<br>We sequenced the genome of an adult Galápagos penguin from Galápagos Islands (provided by Patricia Parker) to a depth of approximately 87x with short reads from a series of libraries with various insert sizes (250bp-20Kb). The assembled scaffolds of high quality sequences total 1.35Gb, with the contig and scaffold N50 values of 70.85Kb and 0.36Mb respectively. We identified 16390 protein-coding genes.
DOI: 10.5524/102372
title: Supporting data for "T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases"

description: Colorectal liver metastasis (CLM) is a leading cause of colorectal cancer mortality, and the response to immune checkpoint inhibition (ICI) in microsatellite stable CRC has been disappointing. Administration of cytotoxic chemotherapy may cause increased density of tumour infiltrating T cells, which has been associated with improved response to ICI. This study aimed to quantify and characterize T cell infiltration in CLM using T cell receptor (TCR) repertoire sequencing. Eighty-five resected CLM from patients included in the Oslo CoMet study were subjected to TCR repertoire sequencing. Thirty-five and 15 patients had received neoadjuvant chemotherapy (NACT) within a short or long interval, respectively, prior to resection, while 35 patients had not been exposed to NACT. T cell fractions were calculated, repertoire clonality was analysed based on Hill evenness curves, and TCR sequential convergence was assessed using network analysis. <br>Increased T cell fractions (10.6% vs 6.3%) were detected in CLM exposed to NACT within a short interval prior to resection, while modestly increased clonality was observed in NACT exposed tumours independently of the timing of NACT administration and surgery. While private clones made up &gt;90% of detected clones, network connectivity analysis revealed that public clones contributed the majority of TCR sequence convergence. <br>TCR repertoire sequencing can be used to quantify T cell infiltration and clonality in clinical samples. This study provides evidence to support chemotherapy-driven T cell clonal expansion in CLM in a clinical context.
DOI: 10.5524/102384
title: Supporting data for "Developmental dynamics of chromatin accessibility during post-implantation development of monkey embryos"

description: Early post-implantation development, especially gastrulation in primates, is accompanied by extensive drastic chromatin reorganization, which remains largely elusive. <br>To delineate the global chromatin landscape and understand the molecular dynamics during this period, single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) was applied to <i>in vitro</i> cultured monkey embryos to investigate the chromatin status. We delineated the cis-regulatory interactions and identified the regulatory networks and key transcription factors involved in epiblast (EPI), hypoblast, and trophectoderm (TE)/trophoblast lineage specification. We also identified the opposing roles of FGF and BMP signaling in pluripotency regulation in EPI cells. The integrative analysis of chromatin accessibility and gene expression revealed that chromatin status activation precedes gene expression during EPI and trophoblast specification. Finally, we revealed the similarity between EPI and TE in terms of gene expression patterns and demonstrated that NR2F2 and PATZ1 are involved in EPI and trophoblast specification during monkey post-implantation development. <br>Our findings provide new resources and insights into dissecting the transcriptional regulatory machinery during primate post-implantation development.
DOI: 10.5281/zenodo.7244070
title: Collection of wing images for conservation of honey bees (Apis mellifera) biodiversity in Europe

description: Identification of honey bee (Apis mellifera) from various parts of the world is essential for protection of their biodiversity. The identification can be based on wing measurements which is inexpensive and easy available. In order to develop such identification there are required reference samples from various parts or the world.


We provide collection of 26481 honey bee fore wing images from 13 countries in Europe: Austria (AT), Croatia (HR), Greece (GR), Moldova (MD), Montenegro (ME), Poland (PL), Portugal (PT), Romania (RO), Serbia (RS), Slovenia (SI), Spain (ES), Turkey (TR). For each country there are three files starting with the two letter country code (indicated earlier in the parentheses): XX-wing-images.zip, XX-raw-coordinates.csv and XX-data.csv, which contain wing images, raw landmark coordinates and geographic coordinates, respectively. Files with prefix EU contain combined data from all countries.


The resolution of the wing images was provided in pixels per meter. If the resolution was not provided it is not known. In those cases only wing shape and not wing size can be analyzed. 


For analysis of the dataset see:


Oleksa, A., Căuia, E., Siceanu, A., Puškadija, Z., Kovačić, M., Pinto, M. A., Rodrigues, P. J., Hatjina, F., Charistos, L., Bouga, M., Prešern, J., Kandemir, İ., Rašić, S., Kusza, S., Tofilski, A. (2023). Honey bee (Apis mellifera) wing images: a tool for identification and conservation. GigaScience, 12, giad019. https://doi.org/10.1093/gigascience/giad019


Oleksa, A., Căuia, E., Siceanu, A., Puškadija, Z., Kovačić, M., Pinto, M. A., Rodrigues, P. J., Hatjina, F., Charistos, L., Bouga, M., Prešern, J., Kandemir, I., Rašić, S., Kusza, S., Tofilski, A. (2023). Apis-wings-EU. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.422.1
description: Acknowledgements
Some samples from Poland were obtained within the framework of a project funded by the State Forests, "Pszczoły wracają do lasu" (Bees Return to the Forest), coordinated by Dr Kazimierz Szabla. Samples from Croatia were obtained during the project "Biodiversity of the honey bee (Apis mellifera carnica) population in the Republic of Croatia (BioBeeCro)" funded by the Paying Agency for Agriculture, Fisheries and Rural Development. Bernadeta Rzeźnicka assisted with the wing measurements. 
This research was funded in part by the National Science Centre, Poland, grant numbers 2021/41/B/NZ9/03153 and 2015/19/B/NZ9/03718. M. Alice Pinto acknowledges Fundação para a Ciência e a Tecnologia for providing financial support from national funds (FCT/MCTES) to CIMO (UIDB/00690/2020 and UIDP/00690/2020) and SusTEC (LA/P/0007/2021).
DOI: 10.5524/102135
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1072

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00001850. Preliminary identification is that it is of the family Poaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 1993150000bp. We have generated 67140000000bp of data, which gives a theoretical coverage of 33.7x.
DOI: 10.5524/102137
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1074

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00001853. Preliminary identification is that it is of the family Poaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 1531140000bp. We have generated 63080000000bp of data, which gives a theoretical coverage of 41.2x.
DOI: 10.5524/102140
title: Genomic data of Nanmaohu Park Taxaceae plant specimen, RL1077

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00001856. Preliminary identification is that it is of the family Taxaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 1688360000bp. We have generated 65680000000bp of data, which gives a theoretical coverage of 38.9x.
DOI: 10.5524/102144
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1081

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00001859. Preliminary identification is that it is of the family Poaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be Not recordedbp. We have generated 79140000000bp of data, which gives a theoretical coverage of x.
DOI: 10.5524/102145
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1082

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00001860. Preliminary identification is that it is of the family Poaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 1041810000bp. We have generated 56640000000bp of data, which gives a theoretical coverage of 54.4x.
DOI: 10.5524/102146
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1083

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00002324. Preliminary identification is that it is of the family Poaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 2169130000bp. We have generated 80220000000bp of data, which gives a theoretical coverage of 37x.
DOI: 10.5524/102147
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1084

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00001861. Preliminary identification is that it is of the family Poaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 6416680000bp. We have generated 76840000000bp of data, which gives a theoretical coverage of 12x.
DOI: 10.5524/102148
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1085

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00001862. Preliminary identification is that it is of the family Poaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 2874470000bp. We have generated 60560000000bp of data, which gives a theoretical coverage of 21.1x.
DOI: 10.5524/102149
title: Genomic data of Nanmaohu Park vascular plant specimen, RL1086

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00002325. Preliminary identification is that it is of the family Poaceae. <br>The K-mer distribution of the sequencing predicted the genome size to be 5501390000bp. We have generated 68100000000bp of data, which gives a theoretical coverage of 12.4x.