cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25442/hku.24042573
title: Supporting data for the thesis entitled "Interpretable deep learning methods for biological sequencing data".

description: This datahub includes sequencing data that were used to develop the new methods for Chapter 2, Chapter 3 and Chapter 4 of the PhD thesis "Interpretable deep learning methods for biological sequencing data"Under the main folder <i><code><strong>Dataset</strong></code></i>, there are three sub-folders. They contain the intermediate results and the code to reproduce the figures for each chapter. Each of the folders is named after <i><code><strong>Dataset(Chapter X)</strong></code></i> and has the structure of:<i><code><strong>Raw </strong></code></i>: The datasets we used to develop the methods are all publicly available. Under the <code>raw</code> folder, you will find a txt file that directs you to the download link for all the raw data.<i><code><strong>Processed </strong></code></i><code>:</code>This folder contains the intermediate results that were built on the public dataset. For example, the analysis results using our proposed methods. In addition, we also uploaded some source data that can be used to draw the figures.<i><code><strong>Script</strong></code></i><i><b> </b></i>: The <code>Script</code> folder has two kinds of code:The source code of the Python package we developed The package can be installed directly.The jupyter notebooks demonstrate how to use our packages and the process of generating figures.
DOI: 10.25442/hku.24042573.v1
title: Supporting data for the thesis entitled "Interpretable deep learning methods for biological sequencing data".

description: This datahub includes sequencing data that were used to develop the new methods for Chapter 2, Chapter 3 and Chapter 4 of the PhD thesis "Interpretable deep learning methods for biological sequencing data"Under the main folder <i><code><strong>Dataset</strong></code></i>, there are three sub-folders. They contain the intermediate results and the code to reproduce the figures for each chapter. Each of the folders is named after <i><code><strong>Dataset(Chapter X)</strong></code></i> and has the structure of:<i><code><strong>Raw </strong></code></i>: The datasets we used to develop the methods are all publicly available. Under the <code>raw</code> folder, you will find a txt file that directs you to the download link for all the raw data.<i><code><strong>Processed </strong></code></i><code>:</code>This folder contains the intermediate results that were built on the public dataset. For example, the analysis results using our proposed methods. In addition, we also uploaded some source data that can be used to draw the figures.<i><code><strong>Script</strong></code></i><i><b> </b></i>: The <code>Script</code> folder has two kinds of code:The source code of the Python package we developed The package can be installed directly.The jupyter notebooks demonstrate how to use our packages and the process of generating figures.
DOI: 10.25442/hku.24043296
title: <i>Supporting data for “</i><i>Improving Preparedness for Emerging Betacoronaviruses: Development of a RT-LAMP-based Diagnostic Assay and a Potential Prophylactic Vaccine</i><i>”</i>

description: The sheet named "COVID-19-LAMP images" contains all images related to the experiment of the developemt of COVID-19-LAMP assay.The sheet named "COVID-19-LAMP data" contains all data generated by COVID-19-LAMP assay.The sheet named "Bat-LAMP images" contains all images related to the experiment of the developemt of bat-LAMP assay.The sheet named "Light microscope images" contains all imsges of cell monolayers photographed by light microscope.The sheet named "Descriptive images" contains all images related to illustration of scientific concepts and experimental designs.The sheet named "Mice weight and survival" contains all data related to the weight change and survival curves of the mice experiment.The sheet named "Histopathoological images" contains all images related to the histopathological analysis of the mice experiment.The sheet named "MERS challenge qPCR" contains the quantified qPCR data of gene expressions of the lung and brain tissues of the mice experiment.The sheet named "MERS challenge TCID50 assay" contains the quantified viral titers of the lung and brain tissues of the mice experiment.The sheet named "MERS SVN assay" contains the quantified 50% neutralization titers of the mice experiment.The sheet named "Flow cytometry gating" contains the flow cytometry sample data used for gating strategy presentation.The sheet named "Flow cytometry result" contains all the flow cytometry result of the mice experiment.The sheet named "Flow tSNE result" contains the tSNE analysis result of the mice experiment.The sheet named "Replication kinetics assay" contains replcation kinetics assay result of the recombinant MERS clones.The sheet named "Protein modedling" contains the analyzed statistics of the protein interaction models by the online server.
DOI: 10.25442/hku.24043296.v1
title: <i>Supporting data for “</i><i>Improving Preparedness for Emerging Betacoronaviruses: Development of a RT-LAMP-based Diagnostic Assay and a Potential Prophylactic Vaccine</i><i>”</i>

description: The sheet named "COVID-19-LAMP images" contains all images related to the experiment of the developemt of COVID-19-LAMP assay.The sheet named "COVID-19-LAMP data" contains all data generated by COVID-19-LAMP assay.The sheet named "Bat-LAMP images" contains all images related to the experiment of the developemt of bat-LAMP assay.The sheet named "Light microscope images" contains all imsges of cell monolayers photographed by light microscope.The sheet named "Descriptive images" contains all images related to illustration of scientific concepts and experimental designs.The sheet named "Mice weight and survival" contains all data related to the weight change and survival curves of the mice experiment.The sheet named "Histopathoological images" contains all images related to the histopathological analysis of the mice experiment.The sheet named "MERS challenge qPCR" contains the quantified qPCR data of gene expressions of the lung and brain tissues of the mice experiment.The sheet named "MERS challenge TCID50 assay" contains the quantified viral titers of the lung and brain tissues of the mice experiment.The sheet named "MERS SVN assay" contains the quantified 50% neutralization titers of the mice experiment.The sheet named "Flow cytometry gating" contains the flow cytometry sample data used for gating strategy presentation.The sheet named "Flow cytometry result" contains all the flow cytometry result of the mice experiment.The sheet named "Flow tSNE result" contains the tSNE analysis result of the mice experiment.The sheet named "Replication kinetics assay" contains replcation kinetics assay result of the recombinant MERS clones.The sheet named "Protein modedling" contains the analyzed statistics of the protein interaction models by the online server.
DOI: 10.25442/hku.24045144
title: Supporting data for “Salt-inducible Kinase 2 : A Potential Metastasis Suppressor in Hepatocellular Carcinoma”

description: Supporting data for the MPhil thesis titled "Salt-inducible Kinase 2 : A Potential Metastasis Suppressor in Hepatocellular Carcinoma". SIK2, a serine/threonine kinase under the AMP-activated protein kinase (AMPK) family, was found to play an important role in the pathogenesis of various cancers affecting the growth, mobility, invasion, and chemosensitivity of cancer cells. However, the function of SIK2 in hepatocellular carcinoma (HCC), one of the leading causes of cancer mortality around the world, has not yet been identified. Therefore, by establishing SIK2 knockout cell lines through the CRISPR/Cas 9 tools, this study explored the role of SIK2 in HCC. Depletion of SIK2 affected proliferation, metastatic properties, and chemoresistance of HCC cells. This dataset includes images taken from western blot for knockout and transfection confirmation, immunohistochemistry on clinical HCC samples, in vitro cell assays and in vivo animal experiment assessing the cell functions of SIK2 knockout cells, with corresponding quantification data.
DOI: 10.25442/hku.24045144.v1
title: Supporting data for “Salt-inducible Kinase 2 : A Potential Metastasis Suppressor in Hepatocellular Carcinoma”

description: Supporting data for the MPhil thesis titled "Salt-inducible Kinase 2 : A Potential Metastasis Suppressor in Hepatocellular Carcinoma". SIK2, a serine/threonine kinase under the AMP-activated protein kinase (AMPK) family, was found to play an important role in the pathogenesis of various cancers affecting the growth, mobility, invasion, and chemosensitivity of cancer cells. However, the function of SIK2 in hepatocellular carcinoma (HCC), one of the leading causes of cancer mortality around the world, has not yet been identified. Therefore, by establishing SIK2 knockout cell lines through the CRISPR/Cas 9 tools, this study explored the role of SIK2 in HCC. Depletion of SIK2 affected proliferation, metastatic properties, and chemoresistance of HCC cells. This dataset includes images taken from western blot for knockout and transfection confirmation, immunohistochemistry on clinical HCC samples, in vitro cell assays and in vivo animal experiment assessing the cell functions of SIK2 knockout cells, with corresponding quantification data.
DOI: 10.25442/hku.24042156
title: Supporting data for "mobile-based behavioral support by ex-smoking peers for smoking cessation: a pragmatic randomized trial"

description: The thesis contained two parts of data: quantitative data and qualitative data.For the quantitative data, we collected data on patterns of tobacco products, daily cigarette consumption, nicotine dependence, past quit attempts, intention to quit, and self-efficacy. The psychological symptoms, including the anxious, depressive symptoms, positive affect, and negative affect, were collected. Participants' sociodemographic characteristics on sex, age, income, education, employment status were also assessed. The biochemical data was also collected.For the qualitative data, we interviewed both the participants and peer supporters to explore their experiences of receiving and delivering smoking cessation support.
DOI: 10.25442/hku.24042156.v1
title: Supporting data for "mobile-based behavioral support by ex-smoking peers for smoking cessation: a pragmatic randomized trial"

description: The thesis contained two parts of data: quantitative data and qualitative data.For the quantitative data, we collected data on patterns of tobacco products, daily cigarette consumption, nicotine dependence, past quit attempts, intention to quit, and self-efficacy. The psychological symptoms, including the anxious, depressive symptoms, positive affect, and negative affect, were collected. Participants' sociodemographic characteristics on sex, age, income, education, employment status were also assessed. The biochemical data was also collected.For the qualitative data, we interviewed both the participants and peer supporters to explore their experiences of receiving and delivering smoking cessation support.
DOI: 10.25442/hku.24054213
title: <b>Supporting data fo</b>r "<b>The major histocompatibility complex, feather microbiome, and body odour in </b><b>Rosy-faced lovebirds </b><i><b>Agapornis roseicollis"</b></i>

description: <i>Agapornis roseicollis </i>feather chemical profile generated using GC-MS. It is the relative abundance data of each compound identified on the feathers. Please refer to the thesis for details. The sample information is written in another file ("GCMS_feather_chemical_sample_info.csv")<i>Agapornis roseicollis </i>16S amplicon sequencing data, containing the count and taxa tables. feather chemical profile generated using GC-MS. It is the relative abundance data of each compound identified on the feathers. Please refer to the thesis for details. The sample information is written in another file ("Microbiome_sample_info.csv")
DOI: 10.25442/hku.24054213.v1
title: <b>Supporting data fo</b>r "<b>The major histocompatibility complex, feather microbiome, and body odour in </b><b>Rosy-faced lovebirds </b><i><b>Agapornis roseicollis"</b></i>

description: <i>Agapornis roseicollis </i>feather chemical profile generated using GC-MS. It is the relative abundance data of each compound identified on the feathers. Please refer to the thesis for details. The sample information is written in another file ("GCMS_feather_chemical_sample_info.csv")<i>Agapornis roseicollis </i>16S amplicon sequencing data, containing the count and taxa tables. feather chemical profile generated using GC-MS. It is the relative abundance data of each compound identified on the feathers. Please refer to the thesis for details. The sample information is written in another file ("Microbiome_sample_info.csv")
DOI: 10.25442/hku.24054795
title: <i><b>Supporting data for </b></i>“Systematic analysis of the sequence-function relationship underlying differentiation and dedifferentiation activity of SOX17”

description: SOX17 has been implicated in both primordial germ cell (PGC) and definitive endoderm differentiation. However, it is unknown how SOX17 (together with OCT4) induces PGC formation. It is known that by engineering SOX17, the aforementioned protein can become a pluripotency inducer- something that is undesired for PGC formation. Thus, the aim of this project is to preliminarily identify and remove any pluripotency-inducing SOX17 high mobility group (HMG) box variants. This dataset provides material regarding the following:<br>(1) Optimization of SOX17 library screening tactics in human embryonic stem cells;<br>(2) Results of screening combinatorial SOX17 HMG box libraries and the SOX17 deep mutational scanning library in pluripotency reprogramming; and<br>(3) Evaluation of SOX17E57 variants separately in pluripotency reprogramming and maintenance.
DOI: 10.25442/hku.24054795.v1
title: <i><b>Supporting data for </b></i>“Systematic analysis of the sequence-function relationship underlying differentiation and dedifferentiation activity of SOX17”

description: SOX17 has been implicated in both primordial germ cell (PGC) and definitive endoderm differentiation. However, it is unknown how SOX17 (together with OCT4) induces PGC formation. It is known that by engineering SOX17, the aforementioned protein can become a pluripotency inducer- something that is undesired for PGC formation. Thus, the aim of this project is to preliminarily identify and remove any pluripotency-inducing SOX17 high mobility group (HMG) box variants. This dataset provides material regarding the following:<br>(1) Optimization of SOX17 library screening tactics in human embryonic stem cells;<br>(2) Results of screening combinatorial SOX17 HMG box libraries and the SOX17 deep mutational scanning library in pluripotency reprogramming; and<br>(3) Evaluation of SOX17E57 variants separately in pluripotency reprogramming and maintenance.
DOI: 10.25442/hku.24049590
title: Supporting data for “Hybrid Organizing for Collaborative Delivery of Real Estate Development Projects in China”

description: Nowadays, more and more Chinese real estate firms deliver projects collaboratively. However, they are facing institutional complexity. This project explores how Chinese real estate firms organize their activities and manage conflicts in response to the institutional complexity in collaborative delivery. This dataset contains two stages data. The first stage data include six preliminary pilot interview transcriptions (Folder1) and 21 field-level interview transcriptions (Folder2). The second stage mainly analysed a case study through case interviews, participant observation, and archival documents. Thus, data include 24 case interview transcriptions (Folder3), fieldnotes of participant observation in the case firm (Folder4), and some important archival documents (Folder5).
DOI: 10.25442/hku.24049590.v1
title: Supporting data for “Hybrid Organizing for Collaborative Delivery of Real Estate Development Projects in China”

description: Nowadays, more and more Chinese real estate firms deliver projects collaboratively. However, they are facing institutional complexity. This project explores how Chinese real estate firms organize their activities and manage conflicts in response to the institutional complexity in collaborative delivery. This dataset contains two stages data. The first stage data include six preliminary pilot interview transcriptions (Folder1) and 21 field-level interview transcriptions (Folder2). The second stage mainly analysed a case study through case interviews, participant observation, and archival documents. Thus, data include 24 case interview transcriptions (Folder3), fieldnotes of participant observation in the case firm (Folder4), and some important archival documents (Folder5).
DOI: 10.25442/hku.24055545
title: <i>Supporting data for</i><i> "</i><i>Modulation of IL-17 Enhances the Efficiency of Anti-PD-1 Therapy in Non-small-cell Lung Cancer"</i>

description: We demonstrated PD-L1 expression in <i>EGFR</i> and<i> KRAS </i>mutant and <i>EGFR/KRAS-</i>wildtype tumor organoids by IFN-γ or co-culture compared with tumor organoids. PD-1 action on T cells and the cytotoxicity of effector T cells through sustained CD107a, perforin and Granzyme B expression in CD8<sup>+</sup><sup> </sup>T cells were detected by flow cytometry after anti-PD-1 treatment. On the other hand, IL-17 concentration in NSCLC patients and non-cancer individuals was detected by ELISA. The level of IL-17 in NSCLC patients' plasma was detected by ELISA. In the tumor organoids-T cells co-culture system, we investigated the concomitant presence of IL-17 and IL-17R expression on <i>EGFR</i>-MT, <i>KRAS</i>-MT<i>E</i><i>G</i><i>FR/KRAS</i>-WT tumor organoids. IL-17R expression on CD4<sup>+</sup><sup> </sup>and CD8<sup>+</sup><sup> </sup>T cells was detected by flow cytometry. Modulation of IL-17 blockade on the efficacy of PD-1 blockade in <i>EGFR</i>-MT, <i>KRAS</i>-MT and <i>EGFR/KRAS</i>-WT NSCLC tumor organoids was detected by flow cytometry.
DOI: 10.25442/hku.24055545.v1
title: <i>Supporting data for</i><i> "</i><i>Modulation of IL-17 Enhances the Efficiency of Anti-PD-1 Therapy in Non-small-cell Lung Cancer"</i>

description: We demonstrated PD-L1 expression in <i>EGFR</i> and<i> KRAS </i>mutant and <i>EGFR/KRAS-</i>wildtype tumor organoids by IFN-γ or co-culture compared with tumor organoids. PD-1 action on T cells and the cytotoxicity of effector T cells through sustained CD107a, perforin and Granzyme B expression in CD8<sup>+</sup><sup> </sup>T cells were detected by flow cytometry after anti-PD-1 treatment. On the other hand, IL-17 concentration in NSCLC patients and non-cancer individuals was detected by ELISA. The level of IL-17 in NSCLC patients' plasma was detected by ELISA. In the tumor organoids-T cells co-culture system, we investigated the concomitant presence of IL-17 and IL-17R expression on <i>EGFR</i>-MT, <i>KRAS</i>-MT<i>E</i><i>G</i><i>FR/KRAS</i>-WT tumor organoids. IL-17R expression on CD4<sup>+</sup><sup> </sup>and CD8<sup>+</sup><sup> </sup>T cells was detected by flow cytometry. Modulation of IL-17 blockade on the efficacy of PD-1 blockade in <i>EGFR</i>-MT, <i>KRAS</i>-MT and <i>EGFR/KRAS</i>-WT NSCLC tumor organoids was detected by flow cytometry.
DOI: 10.25442/hku.24077349
title: supporting data for ALKBH1-regulated 6mA DNA methylation affects human early embryo lineage segregation via TGF-β-signalling pathway using human EPSC as a model

description: The uploaded datasets encompass a diverse range of valuable information. Firstly, they include a collection of cell images that vividly capture the dynamic changes in cell morphology throughout the process of differentiation. These images offer valuable insights into the visual cues and transformations that occur at the cellular level.<br>Secondly, the datasets comprise RT-qPCR data, which provide a comprehensive overview of messenger RNA expression levels. This quantification of gene expression offers a deeper understanding of the molecular mechanisms underlying cellular differentiation, shedding light on the intricate regulatory pathways involved.<br>Furthermore, the dot blotting data within the datasets offer a glimpse into the DNA methylation levels. This information is crucial for unraveling the epigenetic modifications that play a pivotal role in gene regulation during differentiation. By examining the patterns of DNA methylation, researchers can discern the impact of these modifications on cellular behavior and phenotype.<br>Lastly, the datasets include Western blotting data, which furnish valuable insights into the protein expression levels. This quantitative assessment of protein abundance enables researchers to identify key regulatory proteins and signaling pathways associated with cellular differentiation. By understanding the changes in protein expression, scientists can unravel the intricate network of molecular events orchestrating the differentiation process.<br>In summary, the uploaded datasets provide a multidimensional perspective on cellular differentiation, incorporating cell morphology, gene expression, DNA methylation, and protein expression. These comprehensive datasets serve as a valuable resource for researchers aiming to decipher the complex mechanisms governing cellular differentiation and its implications in various biological processes.
DOI: 10.25442/hku.24077349.v1
title: supporting data for ALKBH1-regulated 6mA DNA methylation affects human early embryo lineage segregation via TGF-β-signalling pathway using human EPSC as a model

description: The uploaded datasets encompass a diverse range of valuable information. Firstly, they include a collection of cell images that vividly capture the dynamic changes in cell morphology throughout the process of differentiation. These images offer valuable insights into the visual cues and transformations that occur at the cellular level.<br>Secondly, the datasets comprise RT-qPCR data, which provide a comprehensive overview of messenger RNA expression levels. This quantification of gene expression offers a deeper understanding of the molecular mechanisms underlying cellular differentiation, shedding light on the intricate regulatory pathways involved.<br>Furthermore, the dot blotting data within the datasets offer a glimpse into the DNA methylation levels. This information is crucial for unraveling the epigenetic modifications that play a pivotal role in gene regulation during differentiation. By examining the patterns of DNA methylation, researchers can discern the impact of these modifications on cellular behavior and phenotype.<br>Lastly, the datasets include Western blotting data, which furnish valuable insights into the protein expression levels. This quantitative assessment of protein abundance enables researchers to identify key regulatory proteins and signaling pathways associated with cellular differentiation. By understanding the changes in protein expression, scientists can unravel the intricate network of molecular events orchestrating the differentiation process.<br>In summary, the uploaded datasets provide a multidimensional perspective on cellular differentiation, incorporating cell morphology, gene expression, DNA methylation, and protein expression. These comprehensive datasets serve as a valuable resource for researchers aiming to decipher the complex mechanisms governing cellular differentiation and its implications in various biological processes.