cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/25p-ask-bmg
title: Androsace wulfeniana Sieber ex W. D. J. Koch

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/b3m-03k-w42
title: Miconia sclerophylla Triana

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/crd-n0e-jx2
title: Eryngium L.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/t27-4jw-6e5
title: Bunias erucago L.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/4b0-5w9-8lv
title: Saxifraga stellaris subsp. prolifera (Sternb.) Schönb.-Tem.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/6we-bcy-y9t
title: Erysimum olympicum Boiss.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/ycm-pc0-213
title: Erysimum cheiriflorum Wallr.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5281/zenodo.17053632
title: Dataset for "Quantifying subpercent nuclear TDP‐43 loss in cells and ALS cortex using junction‐specific cryptic exon RT‐qPCR" by Koide, et al.

description: This dataset, including raw experimental data, uncropped Western blot images, and accompanying analysis code, supports the findings of the manuscript "Quantifying subpercent nuclear TDP-43 loss in cells and ALS cortex using junction-specific cryptic exon RT-qPCR" by Koide et al. 

The study focuses on the development and validation of an ultrasensitive RT-qPCR assay for quantifying cryptic exon (CE) splicing, a molecular hallmark of TDP-43 dysfunction in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The novel assay employs a junction-specific primer design targeting STMN2 CE, which significantly enhances sensitivity and dynamic range compared to conventional methods by eliminating pre-mRNA co-amplification.

This repository contains:





Raw_Ct_value.xlsx: An Excel file containing the raw cycle threshold (Ct) values from all RT-qPCR experiments performed in cultured cells (SH-SY5Y, HEK293T) and post-mortem human ALS motor cortex and control tissues. This sheet serves as the primary source for qPCR quantification.




Raw data CSV files (within a Rawdata): CSV files derived from Raw_Ct_value.xlsx or other primary sources, formatted for direct input into the R analysis script. These files contain data used to quantify the expression of STMN2 CE, other TDP-43 responsive CEs, alternative splicing events, and reference genes, and form the basis for generating figures and tables.




Uncropped Western Blot Images: Original, uncropped images for all Western blots presented in the manuscript (e.g., Figure 3B). These images provide the full context for the presented cropped blots, ensuring transparency in data presentation. 




R Markdown file (.Rmd): The R Markdown script used for all statistical analyses, data processing, and figure generation presented in the manuscript. This code allows for the full reproduction of the analyses and figures from the provided CSV data files.




PDF report generated from the R Markdown file (.pdf): This document ("Raw Data and Analysis Code for: Junction-Specific Cryptic Exon RT-qPCR Quantifies Sub-percent Nuclear TDP-43 Loss in Cells and ALS Cortex.pdf") details the R code, package versions used, and sequentially shows the code execution and resulting figures and statistical outputs, corresponding to each figure in the main manuscript.



The aim of sharing this comprehensive dataset and code is to ensure full transparency and reproducibility of our research findings, and to enable further investigation and utilization by the scientific community.

Keywords: TDP-43, Cryptic Exon, STMN2, RT-qPCR, Western Blot, Amyotrophic Lateral Sclerosis, ALS, Frontotemporal Dementia, FTD, Biomarker, Neurodegeneration, Raw Data, R code, Reproducibility.
DOI: 10.3535/haz-kec-2jd
title: Erysimum ghaznicum Cullen & Rech. f.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/sv4-6d3-9p8
title: Puccinellia peisonis (Beck) Jáv.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/xjh-bq9-7qf
title: Puccinellia peisonis (Beck) Jáv.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5281/zenodo.15420811
title: Dataset for "Quantifying subpercent nuclear TDP‐43 loss in cells and ALS cortex using junction‐specific cryptic exon RT‐qPCR" by Koide, et al.

description: This dataset, including raw experimental data, uncropped Western blot images, and accompanying analysis code, supports the findings of the manuscript "Quantifying subpercent nuclear TDP-43 loss in cells and ALS cortex using junction-specific cryptic exon RT-qPCR" by Koide et al. 

The study focuses on the development and validation of an ultrasensitive RT-qPCR assay for quantifying cryptic exon (CE) splicing, a molecular hallmark of TDP-43 dysfunction in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The novel assay employs a junction-specific primer design targeting STMN2 CE, which significantly enhances sensitivity and dynamic range compared to conventional methods by eliminating pre-mRNA co-amplification.

This repository contains:





Raw_Ct_value.xlsx: An Excel file containing the raw cycle threshold (Ct) values from all RT-qPCR experiments performed in cultured cells (SH-SY5Y, HEK293T) and post-mortem human ALS motor cortex and control tissues. This sheet serves as the primary source for qPCR quantification.




Raw data CSV files (within a Rawdata): CSV files derived from Raw_Ct_value.xlsx or other primary sources, formatted for direct input into the R analysis script. These files contain data used to quantify the expression of STMN2 CE, other TDP-43 responsive CEs, alternative splicing events, and reference genes, and form the basis for generating figures and tables.




Uncropped Western Blot Images: Original, uncropped images for all Western blots presented in the manuscript (e.g., Figure 3B). These images provide the full context for the presented cropped blots, ensuring transparency in data presentation. 




R Markdown file (.Rmd): The R Markdown script used for all statistical analyses, data processing, and figure generation presented in the manuscript. This code allows for the full reproduction of the analyses and figures from the provided CSV data files.




PDF report generated from the R Markdown file (.pdf): This document ("Raw Data and Analysis Code for: Junction-Specific Cryptic Exon RT-qPCR Quantifies Sub-percent Nuclear TDP-43 Loss in Cells and ALS Cortex.pdf") details the R code, package versions used, and sequentially shows the code execution and resulting figures and statistical outputs, corresponding to each figure in the main manuscript.



The aim of sharing this comprehensive dataset and code is to ensure full transparency and reproducibility of our research findings, and to enable further investigation and utilization by the scientific community.

Keywords: TDP-43, Cryptic Exon, STMN2, RT-qPCR, Western Blot, Amyotrophic Lateral Sclerosis, ALS, Frontotemporal Dementia, FTD, Biomarker, Neurodegeneration, Raw Data, R code, Reproducibility.
DOI: 10.3535/90r-laq-wfv
title: Erysimum pectinatum Bory & Chaub.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/mk7-80h-ys3
title: Oxytropis campestris subsp. tiroliensis (Fritsch) Leins & Merxm.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/wdr-tjd-lme
title: Avena L.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/vw3-vnm-e48
title: Miconia corallina Spring

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/xa1-9fg-0zt
title: Callianthemum anemonoides (J. Zahlbr.) Endl. ex Heynh.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/3bb-xx7-p81
title: Poa nemoralis L.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/8cv-mxk-x52
title: Phleum phleoides (L.) H. Karst.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/wvh-7vv-y1z
title: Saxifraga blepharophylla A. Kern. ex Hayek

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/3q5-apy-90t
title: Oxytropis campestris subsp. tiroliensis (Fritsch) Leins & Merxm.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/bhk-dxa-dcx
title: Filipendula vulgaris Moench

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/nw7-d7b-dwv
title: Posidonia oceanica (L.) Delile

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/pdm-00h-p9q
title: Puccinellia peisonis (Beck) Jáv.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/490-2as-kle
title: Festuca ovina var. argaea Hack.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/c59-l5j-ae3
title: Cheiranthus parnassi Boiss. & Heldr.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/msb-3qw-qbm
title: Puccinellia peisonis (Beck) Jáv.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/ar2-q5r-hf2
title: Miconia cinchonifolia DC.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/mjk-y9h-s5p
title: Epilobium montanum L.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/rjf-3bf-pq1
title: Saxifraga stellaris subsp. prolifera (Sternb.) Schönb.-Tem.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5517/ccpxy2l
title: CCDC 653420: Experimental Crystal Structure Determination

description: Related Article: Shu-Ting Wu, Yan-Rong Wu, Qing-Qing Kang, Hui Zhang, La-Sheng Long, Zhiping Zheng, Rong-Bin Huang, Lan-Sun Zheng|2007|Angew.Chem.,Int.Ed.|46|8475|doi:10.1002/anie.200703443
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.13140/rg.2.2.21135.82086
title: DL-HMRF code
DOI: 10.3535/esq-yqg-06y
title: Eleocharis R. Br.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/ht3-0ch-ttg
title: Erysimum kunzeanum Boiss. & Reut.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/zn8-1mp-dek
title: Oxytropis campestris subsp. tiroliensis (Fritsch) Leins & Merxm.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5517/ccpxy3m
title: CCDC 653421: Experimental Crystal Structure Determination

description: Related Article: Shu-Ting Wu, Yan-Rong Wu, Qing-Qing Kang, Hui Zhang, La-Sheng Long, Zhiping Zheng, Rong-Bin Huang, Lan-Sun Zheng|2007|Angew.Chem.,Int.Ed.|46|8475|doi:10.1002/anie.200703443
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccpxy4n
title: CCDC 653422: Experimental Crystal Structure Determination

description: Related Article: Shu-Ting Wu, Yan-Rong Wu, Qing-Qing Kang, Hui Zhang, La-Sheng Long, Zhiping Zheng, Rong-Bin Huang, Lan-Sun Zheng|2007|Angew.Chem.,Int.Ed.|46|8475|doi:10.1002/anie.200703443
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.13140/rg.2.2.13481.21600
title: MANUAL DE ABONOS ORGÁNICOS
DOI: 10.3535/3l3-g1e-yrl
title: Carduus personata (L.) Jacq.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/djx-725-aw0
title: Potamogeton L.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/klv-jgb-15m
title: Trichilia P. Browne

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5517/ccpxy5p
title: CCDC 653423: Experimental Crystal Structure Determination

description: Related Article: Shu-Ting Wu, Yan-Rong Wu, Qing-Qing Kang, Hui Zhang, La-Sheng Long, Zhiping Zheng, Rong-Bin Huang, Lan-Sun Zheng|2007|Angew.Chem.,Int.Ed.|46|8475|doi:10.1002/anie.200703443
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/cnc-avv-hjh
title: Puccinellia peisonis (Beck) Jáv.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/md9-qyb-dfd
title: Polygonatum hirtum (Bosc ex Poir.) Pursh

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/zze-81t-tex
title: Thymus boissieri Halácsy

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5517/ccq3qwd
title: CCDC 658994: Experimental Crystal Structure Determination

description: Related Article: J.Clayden, K.R.Hebditch, B.Read, M.Helliwell|2007|Tetrahedron Lett.|48|8550|doi:10.1016/j.tetlet.2007.09.150
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccqhxnr
title: CCDC 670705: Experimental Crystal Structure Determination

description: Related Article: Minghui Bi, Guanghua Li, Jia Hua, Yunling Liu, Xiaomin Liu, Yawei Hu, Zhan Shi, Shouhua Feng|2007|Cryst.Growth Des.|7|2066|doi:10.1021/cg0700824
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.13140/rg.2.2.24753.40803
title: 11 Independent armoured squadron in 1971 war
DOI: 10.13140/rg.2.2.36497.45927
title: 35S:MYB110 transgenic lines in containment glassshouse with purple coloured leaves compared to controls.
DOI: 10.3535/j8z-kd2-tk0
title: Erysimum exaltatum Andrz.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/ll6-aa7-2en
title: Sauvagesia racemosa A. St.-Hil.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/y8t-s71-k5v
title: Androsace wulfeniana Sieber ex W. D. J. Koch

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5517/ccpww7n
title: CCDC 652402: Experimental Crystal Structure Determination

description: Related Article: T.Widjaja, L.Fitjer, A.Pal, H.-G.Schmidt, M.Noltemeyer, C.Diedrich, S.Grimme|2007|J.Org.Chem.|72|9264|doi:10.1021/jo7017558
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccpzyf0
title: CCDC 655353: Experimental Crystal Structure Determination

description: Related Article: Shu-Ting Wu, Yan-Rong Wu, Qing-Qing Kang, Hui Zhang, La-Sheng Long, Zhiping Zheng, Rong-Bin Huang, Lan-Sun Zheng|2007|Angew.Chem.,Int.Ed.|46|8475|doi:10.1002/anie.200703443
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/34s-nfb-bxn
title: Hieracium sylvaticum (L.) Gouan

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/ds4-r1z-j5y
title: Helictotrichon parlatorei (J. Woods) Pilg. x Helictotrichon petzense H. Melzer

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/ks1-qhd-mtl
title: Saxifraga stellaris subsp. prolifera (Sternb.) Schönb.-Tem.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.60797/irj.2025.151.93.1
title: Наименования рыб в хантыйском и мансийском языках

description: Международный научно-исследовательский журнал, Выпуск 1 (151) 2025
DOI: 10.60797/irj.2025.151.93.2
title: Названия рыб в русском, ненецком, хантыйском, мансийском языках

description: Международный научно-исследовательский журнал, Выпуск 1 (151) 2025
DOI: 10.15468/dl.p43uxb
title: Occurrence Download

description: A dataset containing 1471 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Periplaneta lateralis Walker, 1868"
 ]
}

 The dataset includes 1471 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006603-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60797/irj.2025.151.102.1
title: Высота и диаметр ствола изученных видов древесных растений, г. Тюмень

description: Международный научно-исследовательский журнал, Выпуск 1 (151) 2025
DOI: 10.60797/irj.2025.151.104.1
title: Состав сплавов на основе Mn – Cu

description: Международный научно-исследовательский журнал, Выпуск 1 (151) 2025
DOI: 10.15468/dl.e5mu7p
title: Occurrence Download

description: A dataset containing 45622 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "TaxonKey is Chiroptera"
 ]
}

 The dataset includes 45622 records from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000707-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14732036
title: CR2014/2015 Flat-fields (helioprojective)

description: Computed flat-fields in helioprojective coordinates. Flat-fields taken midway through observation. Used for f-mode pipeline (https://github.com/waledeigt/HSSCaster.git).
DOI: 10.5281/zenodo.14732035
title: CR2014/2015 Flat-fields (helioprojective)

description: Computed flat-fields in helioprojective coordinates. Flat-fields taken midway through observation. Used for f-mode pipeline (https://github.com/waledeigt/HSSCaster.git).
DOI: 10.15468/dl.v4szyh
title: Occurrence Download

description: A dataset containing 10271 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ctenopharyngodon idella (Valenciennes, 1844))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10271 records from 201 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000708-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gzj77j
title: Occurrence Download

description: A dataset containing 53 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anathallis aristulata (Lindl.) Luer"
 ]
}

 The dataset includes 53 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000709-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.483a4h
title: Occurrence Download

description: A dataset containing 2379 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lynx pardinus (Temminck, 1827)"
 ]
}

 The dataset includes 2379 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000712-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hk3pa6
title: Occurrence Download

description: A dataset containing 45622 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "TaxonKey is Chiroptera"
 ]
}

 The dataset includes 45622 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000710-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.88cvfx
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is false",
 "StateProvince is one of (North Carolina, South Carolina, Georgia)",
 "TaxonKey is Asclepias tomentosa Elliott"
 ]
}

 The dataset's 1 records were derived from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000704-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8hsynz
title: Occurrence Download

description: A dataset listing the 30 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "HasCoordinate is false",
 "IucnRedListCategory is one of (NT, VU, EN, CR, EW)",
 "TaxonKey is Tracheophyta",
 "Year 2015-2025"
 ]
}

 The dataset's 30 records were derived from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000706-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.