cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13304862
title: Zebrafish embryos time-course, 5'UTRs hnrnpl and egfl6

description: This Zenodo file contains data for the 5′ UTR-hnrnpl-sfGFP and 5′ UTR-egfl6-sfGFP mRNA reporters. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 2 of Reimão-Pinto et al., Dev Cell, 2024.

Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications.

Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.
DOI: 10.5281/zenodo.13304863
title: Zebrafish embryos time-course, 5'UTRs hnrnpl and egfl6

description: This Zenodo file contains data for the 5′ UTR-hnrnpl-sfGFP and 5′ UTR-egfl6-sfGFP mRNA reporters. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 2 of Reimão-Pinto et al., Dev Cell, 2024.

Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications.

Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.
DOI: 10.15468/dl.byfst3
title: Occurrence Download

description: A dataset containing 250416 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Veronica beccabunga L."
 ]
}

 The dataset includes 250416 records from 1366 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016342-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mk22m8
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chalcides delislei (Lataste & Rochebrune, 1876)"
 ]
}

 The dataset includes 24 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0244504-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kf2w6f
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Platyhelminthes",
 "DatasetKey is Merseyside BioBank (verified)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0211461-230224095556074/datasets/export for details.
DOI: 10.15468/dl.wzamhc
title: Occurrence Download

description: A dataset containing 3768 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation)",
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Brycon moorei Steindachner, 1878"
 ]
}

 The dataset includes 3768 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0256784-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2t5j5u
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Platyhelminthes",
 "DatasetKey is Données LPO Réserves Naturelles Nationales - Données des réserves naturelles nationales gérées par la Ligue pour la protection des oiseaux (LPO)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0211487-230224095556074/datasets/export for details.
DOI: 10.15468/dl.gd77uq
title: Occurrence Download

description: A dataset containing 467 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arthropoda",
 "DatasetKey is Inventaires complémentaires des espèces déterminantes ZNIEFF-Données naturalistes sur des périmètres pour créations de nouvelles ZNIEFF ou atualisation de ZNIEFF existantes",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 467 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0218081-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hk9tvu
title: Occurrence Download

description: A dataset containing 312 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hieracium greenei A.Gray"
 ]
}

 The dataset includes 312 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0244534-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.at2era
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arthropoda",
 "DatasetKey is CardObs : Observations naturalistes issues de l'outil CardObs-Inventaire Mollusques ZAC Royon 2020",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0218092-230224095556074/datasets/export for details.
DOI: 10.15468/dl.ngx995
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Living Specimen, Occurrence evidence)",
 "Continent is Asia",
 "Country is Lao People’s Democratic Republic",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Asplenium L."
 ]
}

 The dataset includes 23 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002915-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4fn225
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cerradicola bullata (Benth.) L.P.Queiroz"
 ]
}

 The dataset includes 10 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0222476-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bwfzd6
title: Occurrence Download

description: A dataset containing 4467 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Carthamus lanatus L."
 ]
}

 The dataset includes 4467 records from 213 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0244527-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2gbmne
title: Occurrence Download

description: A dataset containing 253 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Fimbristylis vaginata (R.Br.) Domin"
 ]
}

 The dataset includes 253 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0218095-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k7es8k
title: Occurrence Download

description: A dataset listing the 687 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Country is China",
 "GadmGid is CHN.12_1",
 {
 "or" : [
 "Geometry POLYGON((437.14548 40.48847,445.65504 40.48847,445.65504 47.87455,437.14548 47.87455,437.14548 40.48847))",
 "Geometry POLYGON((457.0079 15.8346,481.66183 15.8346,481.66183 36.30059,457.0079 36.30059,457.0079 15.8346))"
 ]
 },
 "HasCoordinate is true",
 "Year 2020-2023"
 ]
}

 The dataset's 687 records were derived from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0068212-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qtv7yg
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arthropoda",
 "DatasetKey is Mollusc records for specimens held at the Stoke-on-Trent Potteries Museum",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0218104-230224095556074/datasets/export for details.
DOI: 10.15468/dl.37xeh4
title: Occurrence Download

description: A dataset listing the 427 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-70.36485 19.12789,-70.16716 19.12789,-70.16716 19.4053,-70.36485 19.4053,-70.36485 19.12789))",
 "HasCoordinate is true"
 ]
}

 The dataset's 427 records were derived from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0256799-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kdxbqz
title: Occurrence Download

description: A dataset containing 87 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Galactia filiformis (Jacq.) Benth."
 ]
}

 The dataset includes 87 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0222507-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.89rv8u
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hieracium gratiosum Wiinst."
 ]
}

 The dataset includes 18 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0244525-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m5qdnn
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Galium vartanii Grossh."
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0224006-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kqcvtz
title: Occurrence Download

description: A dataset containing 3055 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Canada",
 "GadmGid is CAN.11_1",
 "TaxonKey is Asclepias syriaca L."
 ]
}

 The dataset includes 3055 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0230444-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6grp23
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Platyhelminthes",
 "DatasetKey is Diveboard - Scuba diving citizen science observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0211476-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.za3a92
title: Occurrence Download

description: A dataset containing 733758 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year 2020-2023"
 ]
}

 The dataset includes 733758 records from 365 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0244528-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cc87sm
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Platyhelminthes",
 "DatasetKey is AKG-Gelände in Bensheim",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0211474-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cuv4s8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arthropoda",
 "DatasetKey is CardObs : Observations naturalistes issues de l'outil CardObs-INVENTAIRE DE LA MALACOFAUNE DE LA RÉSERVE NATURELLE NATIONALE DES VALLÉES DE LA GRANDE-PIERRE ET VITAIN",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0218074-230224095556074/datasets/export for details.
DOI: 10.15468/dl.wr37qx
title: Occurrence Download

description: A dataset listing the 2 species recorded in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Trachurus murphyi Nichols, 1920"
 ]
}

 The dataset's 2 records were derived from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046546-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e6praq
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Platyhelminthes",
 "DatasetKey is Crayfish data update for Environment Agency Thames Region March 2009",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0211518-230224095556074/datasets/export for details.
DOI: 10.15468/dl.9vgnn4
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leiospora eriocalyx (Regel & Schmalh.) F.Dvořák"
 ]
}

 The dataset includes 26 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005609-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ngwr7h
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Platyhelminthes",
 "DatasetKey is Lajitietokeskus/FinBIF - Notebook, general observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 14 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0211473-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.27fdxq
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Jumellea alionae P.J.Cribb"
 ]
}

 The dataset includes 6 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0256801-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b6ag6b
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Platyhelminthes",
 "DatasetKey is Royal Netherlands Institute for Sea Research (NIOZ) - Kom Fyke Mokbaai",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0211502-230224095556074/datasets/export for details.
DOI: 10.15468/dl.y6zcvn
title: Occurrence Download

description: A dataset containing 1744 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leiocarpa websteri (S.Moore) Paul G.Wilson"
 ]
}

 The dataset includes 1744 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005606-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2ywc8p
title: Occurrence Download

description: A dataset containing 1804 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sphyradium doliolum (Bruguière, 1792)"
 ]
}

 The dataset includes 1804 records from 95 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002907-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.