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364 results for “developmental stage”
Alkanna tinctoria (L.) Tausch roots in different soils and developmental stages, HPLC peak areas of alkannins/shikonins
<p>Table of peak areas of alkannins detected in the HPLC-UV/Vis analysis of extracts of <em>Alkanna tinctoria</em> (L.) Tausch root samples cultivated in the greenhouse in various soils. Samples come from four different stages of plant growth.</p>
Soil pH, developmental stages and geographical origin differently influence the root metabolomic diversity and root-related microbial diversity of Echium vulgare from native habitats
<p>R Studio codes and ASV table used to analyze the microbiome data of our Echium vulgare microbial ecology experiment. </p>
Developmental stages of bud primordia in Vaccinium vitis-idaea across 16 sites in Interior Alaska 2017-2019
This dataset contains the stages of the flower bud primordia (buds prior to anthesis) for Vaccinium vitis-idaea at 19 sites in the Fairbanks area for two cohorts (one initiated in 2017 and matured in 2018, and one initated in 2018 and matured in 2019). Developmental stages were tracked from early June to early October, and then again the following May. Buds were classified as basal, middle, or apical. Developmental stages are based on scanning lectron microscopy. Associated data describe temperature for each interval (period between collection dates), along with site characteristics (location, canopy cover, and depth of thaw in late May).
Dataset of examples of Drosophila epithelia at different developmental stages
<p><strong>File list</strong></p> <p>A) notum1_GFP.TIF and notum1_mCherry.TIF</p> <p>B) notum2_GFP.tif and notum2_mCherry.tif</p> <p>C) wing_disc1.tif</p> <p>D) wing_disc2.tif</p> <p><strong>Samples</strong></p> <p>A-B) Posterior region of live drosophila pupal notum. All the cells express E-Cadherin::GFP, and a clonal subpopulation of them express active Yorkie and nuclear mCherry protein.</p> <p>C-D) Drosophila wing imaginal discs from L3 larval stage stained for (C) E-cadherin (green) and GFP (clone, magenta), (D) E-cadherin (green) and phospho-histone H3 (magenta)</p> <p><strong>Imaging conditions</strong></p> <p>(A) was done on a confocal spinning disk microscope with a 40X oil objective. (B,C,D) images were acquired using a Zeiss LSM 880 confocal microscope, equipped with an oil immersion objective (Plan-Apochromat 40x/1.3 Oil DIC UV-IR M27). (A-B) Stacks were generated with a Z interval of 1.5 um, 0.5 for (C) and 1 um for (D). (A) pixel size is 0.28um. (B-D) pixel size is 0.35um.</p>
Figure 17 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 17. Selected dentaries of Thylacinus showing differences in the diastemata between the premolars as the effect of increasing age. A, subadult (in labial view) with m3 erupted, but not m4. Only slight suggestions of diastemata are evident between the premolars; B (lingual view) and C (labial view), showing later stages of m4 eruption and the increase of diastemata in adults.
Figure 16 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 16. Later stages of early eruption in Thylacinus showing the presence and early loss of dp3 in the dentary. A, Part of the dentary (CU A6 7/10), redrawn from Moeller (1968), showing the erupted dp3, the unerupted successor p3 in its alveolar crypt, immediately anterior to dp3, and the erupting m1. The erupting dp1 and dp2 are also labeled; B, A slightly later stage of eruption in the dentary (USNM 115365) shows that the dp3 has been lost, and successor p3 is in early eruption. The m1 is now almost completely erupted. c indicates lower successional canine in B.
Figure 13 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 13. Computed tomography images from the supplementary data of Newton et al. (2018). A, section of the skull and dentition from TMAG A931, a thylacine pouch young of 35 - 37 days old; B, Section of the skull and dentition from TMAG A930, a thylacine pouch young of 66 - 67 days old. Scale bars are 5 mm. C, canine; dP1, deciduous first premolar; dP2, deciduous second premolar; dP3, deciduous third premolar; M1, first molar; P3, successional third premolar.
Figure 12 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 12. Section through dp3 and its successor p3. Only a small fragment of the lingual successional lamina is evident. Compare this single section with the camera lucida drawings in Figure 11. dp3, deciduous third premolar; lsl, lingual successional lamina; p3, successional third premolar.
Figure 10 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 10. Section through the level of the metacone on M1, with thick enamel on its apex and disrupted dentin; d, dentin; e, enamel; me, metacone apex.
Figure 11 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 11. Camera lucida drawings of dp3 and p3 in the dentary, at different planes of section. A, The lingual successional lamina is fragmented, but still largely intact, between the small dp3 and its larger successional p3; B, The small dp3 is evident with its dentin and enamel, and its primary dental lamina connection to the oral epithelium is fragmented but still evident. The section through the successor p3 is not central, but it shows the fragmented lingual successional lamina between the two teeth. A, ameloblasts; AB, alveolar bone; D, dentin; dp3, deciduous third premolar; E, enamel; O, odontoblasts; OE, oral epithelium; P, dental papilla; p3, successor third premolar; PL, primary dental lamina; SL, lingual successional lamina; SR, stellate reticulum.
Figure 6 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 6. Longitudinal section through dP2, with disrupted dentin and well - developed enamel. d, dentin; e, enamel.
Figure 9 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 9. Section of M1, at level of paracone. A, paracone with overlying epithelial nodule; B, paracone at more central level, lacking the epithelial nodule; en, epithelial nodule; pa, paracone apex.
Figure 3 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 3. Histological section of I1 in Thylacinus, in middle bell stage. dp, dental papilla; en, epithelial nodule; o, oral epithelium; pdl, primary dental lamina.
Figure 1 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 1. Thylacinus (71.1 mm Head Length) pouch young, with unerupted dentition; redrawn from Flower, 1867. C, upper and lower canine; dP3, upper and lower deciduous third premolar; M1, upper and lower first molar; P3, upper and lower successional third premolar.
Figure 5 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 5. Longitudinal section through large successional upper canine, with disrupted dentin and well -developed enamel. d, dentin; e, enamel.
Figure 8. Late bell stage successor P3 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 8. Late bell stage successor P3. This tooth lies anterior to dP3 and it lacks dentin and enamel. lsl, short segment of lingual successional lamina; t, tongue.
Figure 2. Sibling pouch young thylacines. A, NMV C5754 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 2. Sibling pouch young thylacines. A, NMV C5754, male specimen sectioned for histology images; B, NMV C 5757, female specimen, used by Feigin et al. (2018) for genomic analysis.
Figure 14 in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 14. Images of the head, skull, and dentition of the thylacine pouch young from the Australian Museum (AM P 762). A, X-ray of the skull, showing deciduous and successional teeth in varying stages of development and early eruption; B, Head and upper body of the pouch young, prior to X-ray analysis; C, Higher magnification of a portion of the X-ray shown in figure A, with emphasis on the erupted lower dp3, and the unerupted but larger successional p3 immediately anterior to it.
Figure 4. Longitudinal section through I4 and transverse section through smaller I3. e in Microscopic analysis of the developing dentition in the pouch young of the extinct marsupial Thylacinus cynocephalus, with an assessment of other developmental stages and eruption
Figure 4. Longitudinal section through I4 and transverse section through smaller I3. e, disrupted enamel.
Platynereis dumerilii full-length transcriptome of developmental stages
<p>To generate a high-quality full-length transcriptome for the annelid <em>Platynereis dumerilii</em>, we collected samples from representative developmental stages, from unfertilized eggs to 5 days post-fertilization. Each sample consisted of a bulk mix from 1 to 5 batches of embryos fertilized by different parents. We incubated all batches at 18 degrees Celsius until the desired time point, then collected the embryos into a clean tube and snap-froze them in liquid nitrogen with as little seawater as possible. The samples were stored at -80 degrees Celsius until RNA extraction. We extracted total RNA from the samples using a Trizol protocol. After measuring the RNA concentration with NanoDrop, we created a bulk RNA mix by combining 1 µL from each sample into a new tube. We gave the sample to the Sequencing and Genotyping facility of the Max Planck Institute of Molecular Cell Biology and Genetics, who ran aliquots of this bulk mix through a Bioanalyzer and gel electrophoresis. They found no evidence of RNA degradation. From this sample, they prepared PacBio Iso-Seq libraries using the Express Template Prep Kit 2.0 and sequenced full-length transcripts on a SMRT 8M Cell for 30 hours using a PacBio Sequel II System. They processed the raw movie subreads with SMRT Analysis software, following the Iso-Seq v3 workflow to generate representative circular consensus sequences, demultiplex and remove primers, trim poly(A) tails, and remove concatemers. After transcript clustering and merging, the resulting dataset contained 176,122 polished high-quality isoforms. Using Cogent, we removed redundant isoforms and obtained a dataset with 117,524 transcripts. From this, we generated a dataset containing only the longest isoform for each gene, with 70,003 sequences in total. We calculated descriptive metrics using Transrate. To estimate their completeness, we used BUSCO for metazoa and obtained a score of 85%. Finally, we annotated the longest-isoform dataset using EnTAP. About 85% of the transcripts have a coding sequence. We obtained annotations for 67% of the sequences, while 33% have remained unannotated.</p> <h2>Datasets</h2> <table> <tbody> <tr> <td><strong>file name</strong></td> <td><strong>file size (zipped)</strong></td> <td><strong>sequences</strong></td> <td><strong>description</strong></td> </tr> <tr> <td><a href="https://zenodo.org/records/14250773/files/0-Pdum_workflow.zip?download=1">0-Pdum_workflow.zip</a> (folder)</td> <td>3.40 GB</td> <td>-</td> <td>entire pipeline with notebook entries and analyses</td> </tr> <tr> <td><a href="https://zenodo.org/records/14250773/files/1-Pdum_hq_isoforms.zip?download=1">1-Pdum_hq_isoforms.zip</a> (fasta)</td> <td>180.30 MB</td> <td>176,122</td> <td>polished high-quality isoforms from CCS</td> </tr> <tr> <td><a href="https://zenodo.org/records/14250773/files/2-Pdum_co_isoforms.zip?download=1">2-Pdum_co_isoforms.zip</a> (fasta)</td> <td>70.68 MB</td> <td>117,524</td> <td>non-redundant polished high-quality isoforms</td> </tr> <tr> <td><a href="https://zenodo.org/records/14250773/files/3-Pdum_co_longest.zip?download=1">3-Pdum_co_longest.zip</a> (fasta)</td> <td>54.85 MB</td> <td>70,003</td> <td>longest of non-redundant polished high-quality isoforms</td> </tr> <tr> <td><a href="https://zenodo.org/records/14250773/files/4-Pdum_co_longest_annotations.zip?download=1">4-Pdum_co_longest_annotations.zip</a> (tsv)</td> <td>34.37 MB</td> <td>70,003 (46,635 annotated)</td> <td>annotations for longest-isoform dataset</td> </tr> </tbody> </table> <p> </p>
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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.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.