Computational biology
View article: Hub genes in a pan-cancer co-expression network show potential for predicting drug responses
Hub genes in a pan-cancer co-expression network show potential for predicting drug responses Open
Dataset 1. Gene co-expression network data. It contains network nodes, weighted network and list of hubs. Dataset 2. qPCR data from independent validation, including MIQE and additional information.
View article: sRNA_seq_clean_thrips_leafdiscs_timeseries
sRNA_seq_clean_thrips_leafdiscs_timeseries Open
2023-03 Timeseries experiment with clean thrips on leafdiscs of tomato MoneyMaker plants. srna and mrna were extracted with the kit 'NucleoSpin miRNA, Mini kit for miRNA and RNA purification'. contains (see metadata file for more info): - …
View article: Distance matrix showing the distance between twenty-three eight most similar sequences from NCBI GenBank.
Distance matrix showing the distance between twenty-three eight most similar sequences from NCBI GenBank. Open
Distance matrix showing the distance between twenty-eight most similar sequences from NCBI GenBank.
View article: Differentiated genomic footprints and connections inferred from 440 Hmong-Mien genomes suggest their isolation and long-distance migration
Differentiated genomic footprints and connections inferred from 440 Hmong-Mien genomes suggest their isolation and long-distance migration Open
Background: The underrepresentation of Hmong-Mien (HM) people in Asian genomic studies has hindered our comprehensive understanding of the full landscape of their evolutionary history and complex t…
View article: Reference transcriptome for the siphonophore Marrus sp.
Reference transcriptome for the siphonophore Marrus sp. Open
Long read--PacBio IsoSeq--reference transcriptome for the siphonophore Marrus sp.
View article: oropharyngeal swabs 16S rRNA sequencing from PDAC/control
oropharyngeal swabs 16S rRNA sequencing from PDAC/control Open
View article: oropharyngeal swabs 16S rRNA sequencing from PDAC/control
oropharyngeal swabs 16S rRNA sequencing from PDAC/control Open
View article: Pulldown shotgun proteomics Arabidopsis STOP1
Pulldown shotgun proteomics Arabidopsis STOP1 Open
Pulldown shotgun proteomics Arabidopsis STOP1
View article: Pulldown shotgun proteomics Arabidopsis STOP1
Pulldown shotgun proteomics Arabidopsis STOP1 Open
Pulldown shotgun proteomics Arabidopsis STOP1
View article: Mass spectrometry imaging (MSI) datasets
Mass spectrometry imaging (MSI) datasets Open
Mass spectrometry imaging (MSI) datasets.
View article: Mass spectrometry imaging (MSI) datasets
Mass spectrometry imaging (MSI) datasets Open
Mass spectrometry imaging (MSI) datasets.
View article: Comprehensive RNA-seq analysis of colorectal cancer in a Korean cohort
Comprehensive RNA-seq analysis of colorectal cancer in a Korean cohort Open
Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide, and understanding the molecular mechanisms underlying CRC development and progression is critical for developing effective treatments. In this study, we perf…
View article: Spatial transcriptomic profiling of intact and spinal cord–injured mouse spinal cords using CosMx SMI
Spatial transcriptomic profiling of intact and spinal cord–injured mouse spinal cords using CosMx SMI Open
This study investigates the temporal remodeling of the immune microenvironment after spinal cord injury (SCI) using Nanostring CosMx SMI high-plex spatial molecular imaging. Spinal cord tissues were collected from female C57BL/6J mice (8 w…
View article: Cell-Type-Specific Transcriptomic Signatures in Prefrontal Cortex Reveal lncRNA-mediated Gene Silencing and Enhancer Activities Contributing to the Pathophysiology of Major Depressive Disorder
Cell-Type-Specific Transcriptomic Signatures in Prefrontal Cortex Reveal lncRNA-mediated Gene Silencing and Enhancer Activities Contributing to the Pathophysiology of Major Depressive Disorder Open
Table S1: lncRNA microarray expression data. Table S2: mRNA microarray expression data. Table S3: lncRNA Differential expression. Table S4: mRNA differential expression. Table S5: Inhibitory regulation of lncRNAs on mRNAs. Table S6: Cellul…
View article: Cell-Type-Specific Transcriptomic Signatures in Prefrontal Cortex Reveal lncRNA-mediated Gene Silencing and Enhancer Activities Contributing to the Pathophysiology of Major Depressive Disorder
Cell-Type-Specific Transcriptomic Signatures in Prefrontal Cortex Reveal lncRNA-mediated Gene Silencing and Enhancer Activities Contributing to the Pathophysiology of Major Depressive Disorder Open
Table S1: lncRNA microarray expression data. Table S2: mRNA microarray expression data. Table S3: lncRNA Differential expression. Tab…
View article: Script repository: Polyamine-dependent metabolic shielding regulates alternative splicing
Script repository: Polyamine-dependent metabolic shielding regulates alternative splicing Open
Polyamine-dependent metabolic shielding regulates alternative splicing Analysis of the alternative splicing changes in all RNA-seq datasets available in GEO database with the identifiers GSE301290, GSE244378 and GSE255769…
View article: OpenFISH enables integrated high-resolution spatial transcriptomics and metabolomics on a single tissue section
OpenFISH enables integrated high-resolution spatial transcriptomics and metabolomics on a single tissue section Open
Datasets of paper "OpenFISH enables integrated high-resolution spatial transcriptomics and metabolomics on a single tissue section"
View article: OpenFISH enables integrated high-resolution spatial transcriptomics and metabolomics on a single tissue section
OpenFISH enables integrated high-resolution spatial transcriptomics and metabolomics on a single tissue section Open
Datasets of paper "OpenFISH enables integrated high-resolution spatial transcriptomics and metabolomics on a single tissue section"
View article: Alzheimer's disease-induced phagocytic microglia express specific profile of coding and non-coding RNAs
Alzheimer's disease-induced phagocytic microglia express specific profile of coding and non-coding RNAs Open
This repository contains the data and the code used in Flavia's project. A folder can contain the starting raw data in "data", the R scripts in order of execution (op1, op2 ..) and the "output" folder that contains the final processed data…
View article: Alzheimer's disease-induced phagocytic microglia express specific profile of coding and non-coding RNAs
Alzheimer's disease-induced phagocytic microglia express specific profile of coding and non-coding RNAs Open
This repository contains the data and the code used in Flavia's project. A folder can contain the starting raw data in "data", the R scripts in order of execution (op1, op2 ..) and the "output" folder that contains the final processed data…
View article: Z8 manuscript omics data
Z8 manuscript omics data Open
Bulk CRISPR, scCRISPR, scRNA-seq, ATAC-seq, CUT&RUN data
View article: Z8 manuscript omics data
Z8 manuscript omics data Open
Bulk CRISPR, scCRISPR, scRNA-seq, ATAC-seq, CUT&RUN data
View article: CITePuro-seq on induced T regulatory cells
CITePuro-seq on induced T regulatory cells Open
This dataset contains single-cell CITE-Puro-seq data from induced regulatory T cells (iTregs) generated in vitro. The experiment integrates mRNA expression and puromycin-based protein incorporation to capture both transcriptional and trans…
View article: CITePuro-seq on induced T regulatory cells
CITePuro-seq on induced T regulatory cells Open
This dataset contains single-cell CITE-Puro-seq data from induced regulatory T cells (iTregs) generated in vitro. The experiment integrates mRNA expression and puromycin-based protein incorporation to capture both transcriptional and trans…
View article: AI-Guided Discovery of Universal Atherosclerosis Convergence Pathways and Multi-Target Therapeutic Interventions
AI-Guided Discovery of Universal Atherosclerosis Convergence Pathways and Multi-Target Therapeutic Interventions Open
This computational framework presents ATHERO-RESTORE v1.0, a comprehensive AI-guided approach to identifying universal atherosclerosis convergence pathways and designing multi-target therapeutic interventions for cardiovascular disease (CV…
View article: Separable roles for Microprocessor and its cofactors ERH and SAFB1/2 during microRNA cluster assistance
Separable roles for Microprocessor and its cofactors ERH and SAFB1/2 during microRNA cluster assistance Open
Results of the smallRNA analysis pipeline used in "Separable roles for Microprocessor and its cofactors ERH and SAFB1/2 during microRNA cluster assistance". 20251028_mirbase_results.tar.gz : GZIP archive of the analysis pipeline results. N…
View article: Separable roles for Microprocessor and its cofactors ERH and SAFB1/2 during microRNA cluster assistance
Separable roles for Microprocessor and its cofactors ERH and SAFB1/2 during microRNA cluster assistance Open
Results of the smallRNA analysis pipeline used in "Separable roles for Microprocessor and its cofactors ERH and SAFB1/2 during microRNA cluster assistance". 20251028_mirbase_results.tar.gz
View article: Custom scripts used in Vicia faba VF8137 genome
Custom scripts used in Vicia faba VF8137 genome Open
Box.R-A R script inorder to plot some box pictures. change_table.pl-Change some special format of files. hap_fig.R-Drawing haplotypes. makeagpfromscaffold.change.pl-Split genome to contig sequence. manhantan.R-Ploting some manhattan pictur…
View article: Single-cell data: Antigen-reactive CD4 T cells after SARS-CoV-2 vaccination show divergent phenotypic states with or without restimulation
Single-cell data: Antigen-reactive CD4 T cells after SARS-CoV-2 vaccination show divergent phenotypic states with or without restimulation Open
Understanding T cell fate requires precise knowledge of antigen reactivity. For CD4+ T cells, conventional identification of antigen reactivity by peptide restimulation relies on cellular activation, but thereby also introduces…
View article: De novo assembled transcriptome of Red Rubin (Ocimum basilicum) cultivar
De novo assembled transcriptome of Red Rubin (Ocimum basilicum) cultivar Open
RNA-Seq libraries were prepared and sequenced on an Illumina NovaSeq platform (Genewiz, Leipzig, Germany), generating 150 bp paired-end reads. Raw sequencing reads are available in the National Center for Biotechnology Information (N…