Genetics
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: 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: 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 trait architecture. South China is a multi-…
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: 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: 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: 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: 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: Human iPSC-derived microglia carrying LRRK2-G2019 mutation show Parkinson's disease related transcriptional profile and functions
Human iPSC-derived microglia carrying LRRK2-G2019 mutation show Parkinson's disease related transcriptional profile and functions Open
This repository contains the data and the code used in Ohtone Sohvi'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 processe…
View article: Human iPSC-derived microglia carrying LRRK2-G2019 mutation show Parkinson's disease related transcriptional profile and functions
Human iPSC-derived microglia carrying LRRK2-G2019 mutation show Parkinson's disease related transcriptional profile and functions Open
This repository contains the data and the code used in Ohtone Sohvi'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 processe…
View article: Genomic analysis of T cell receptors in a cohort of Lynch Syndrome carriers distinguishes pre-malignant and malignant status
Genomic analysis of T cell receptors in a cohort of Lynch Syndrome carriers distinguishes pre-malignant and malignant status Open
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: The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons.
The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons. Open
Paramecia belong to the ciliate phylum of unicellular eukaryotes characterized by nuclear dimorphism. A diploid germline micronucleus (MIC) transmits genetic information across sexual generations. A polyploid transcriptionally active…
View article: The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons.
The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons. Open
Paramecia belong to the ciliate phylum of unicellular eukaryotes characterized by nuclear dimorphism. A diploid germline micronucleus (MIC) transmits genetic information across sexual generations. A polyploid transcriptionally active somat…
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: Repetitive DNA Dynamics, Phylogenetic Relationships and Divergence Times in Andean Ctenomys (Rodentia: Ctenomyidae).
Repetitive DNA Dynamics, Phylogenetic Relationships and Divergence Times in Andean Ctenomys (Rodentia: Ctenomyidae). Open
The genus Ctenomys comprises a group of rodents with remarkable karyotypic variability linked to the distribution of repetitive sequences and rearrangements. We analyzed the distribution and variation of repetitive DNA in tw…
View article: Repetitive DNA Dynamics, Phylogenetic Relationships and Divergence Times in Andean Ctenomys (Rodentia: Ctenomyidae).
Repetitive DNA Dynamics, Phylogenetic Relationships and Divergence Times in Andean Ctenomys (Rodentia: Ctenomyidae). Open
The genus Ctenomys comprises a group of rodents with remarkable karyotypic variability linked to the distribution of repetitive sequences and rearrangements. We analyzed the distribution and variation of repetitive DNA in two parapatric An…
View article: T2T genome assembly of Micropterus salmoides (female and male)
T2T genome assembly of Micropterus salmoides (female and male) Open
The largemouth bass (Micropterus salmoides, LMB) is a globally significant species in aquaculture and fisheries. Since its introduction to China in 1983, its aquaculture production has surged, reaching 802,486 metric tons in 2…
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…
View article: Mapping single cell eQTLs by using MatrixEQTL with pseudo-bulk cell type
Mapping single cell eQTLs by using MatrixEQTL with pseudo-bulk cell type Open
These scripts are implementing a two-step approach for detecting eQTL and conditional eQTL analysis for cell type gene expression in single cell RNA seq study. Relevant R packages: SVA (version 3.52.0, DOI: 10.18129/B9.bioc.sva), MatrixEQT…
View article: On L¹ and time-optimal state transitions in piecewise linear models of gene-regulatory networks
On L¹ and time-optimal state transitions in piecewise linear models of gene-regulatory networks Open
View article: A Study of HSPA1A and DNAJB1 regulate NELF condensate dynamicity to safeguard transcriptional recovery under heat stress. Jiang et al
A Study of HSPA1A and DNAJB1 regulate NELF condensate dynamicity to safeguard transcriptional recovery under heat stress. Jiang et al Open
View article: A Study of HSPA1A and DNAJB1 regulate NELF condensate dynamicity to safeguard transcriptional recovery under heat stress. Jiang et al
A Study of HSPA1A and DNAJB1 regulate NELF condensate dynamicity to safeguard transcriptional recovery under heat stress. Jiang et al Open
View article: Deep genetic sequencing analyses of the mTOR and endocannabinoid signaling pathways in patients with focal cortical dysplasia identify an unprecedented CNR1 truncating variant
Deep genetic sequencing analyses of the mTOR and endocannabinoid signaling pathways in patients with focal cortical dysplasia identify an unprecedented CNR1 truncating variant Open