Pinned Repositories
40Tcells
Paired rRNA-depleted and polyA-selected RNA sequencing from primary CD4 T cell of 40 healthy individuals with multi-omics data
COVID-19
Effect of genetic variants in COVID-19
DEMINERS
hemato
Short-read and long-read RNA sequencing of mouse haematopoietic stem cells at bulk and single-cell levels
inferCC
Lung cancer 10X analysis
MA-ARDS
MeDAS
MeDAS: a Metazoan Developmental Alternative Splicing database
Neuron
During brain development, neural stem cells (NSCs) undergo multiple fate-switches to generate various neuronal subtypes and glial cells, exhibiting distinct transcriptomic profiles at different stages. Despite the extensive transcriptomic characterization of human and mouse brain cells at bulk and single-cell levels, full-length transcriptomic datasets of NSCs across different neurodevelopmental stages under similar experimental settings are lacking, which is essential for uncovering stage-specific transcriptional and post-transcriptional mechanisms underlying the fate commitment of NSCs. Here, we report the full-length transcriptome of mouse NSCs at five different stages during embryonic and postnatal development. We used fluorescent-activated cell sorting (FACS) to isolate CD133+Blbp+ NSCs from C57BL/6 transgenic mice that express enhanced green fluorescent protein (EGFP) under the control of a Blbp promoter. Integrating Smart-seq2 RNA-seq and Oxford Nanopore full-length RNA-seq, we created a transcriptomic dataset of gene and isoform expression profiles in NSCs at embryonic days 15.5, 17.5, and postnatal days 1.5, 8, and 60. This dataset provides a detailed characterization of full-length transcripts in NSCs at distinct developmental stages, and could be used as a resource for the neuroscience community to study NSC fate determination, neural development, and disease.
RNA_Seq_protocol
RNA-Seq protocol of HISAT2-StringTie-Ballgown
SCAPE
Single Cell Alternative Polyadenylation using Expectation-maximization
ChenlinLab's Repositories
LuChenLab/inferCC
Lung cancer 10X analysis
LuChenLab/SCAPE
Single Cell Alternative Polyadenylation using Expectation-maximization
LuChenLab/40Tcells
Paired rRNA-depleted and polyA-selected RNA sequencing from primary CD4 T cell of 40 healthy individuals with multi-omics data
LuChenLab/COVID-19
Effect of genetic variants in COVID-19
LuChenLab/DEMINERS
LuChenLab/Neuron
During brain development, neural stem cells (NSCs) undergo multiple fate-switches to generate various neuronal subtypes and glial cells, exhibiting distinct transcriptomic profiles at different stages. Despite the extensive transcriptomic characterization of human and mouse brain cells at bulk and single-cell levels, full-length transcriptomic datasets of NSCs across different neurodevelopmental stages under similar experimental settings are lacking, which is essential for uncovering stage-specific transcriptional and post-transcriptional mechanisms underlying the fate commitment of NSCs. Here, we report the full-length transcriptome of mouse NSCs at five different stages during embryonic and postnatal development. We used fluorescent-activated cell sorting (FACS) to isolate CD133+Blbp+ NSCs from C57BL/6 transgenic mice that express enhanced green fluorescent protein (EGFP) under the control of a Blbp promoter. Integrating Smart-seq2 RNA-seq and Oxford Nanopore full-length RNA-seq, we created a transcriptomic dataset of gene and isoform expression profiles in NSCs at embryonic days 15.5, 17.5, and postnatal days 1.5, 8, and 60. This dataset provides a detailed characterization of full-length transcripts in NSCs at distinct developmental stages, and could be used as a resource for the neuroscience community to study NSC fate determination, neural development, and disease.
LuChenLab/ggsashimi
Command-line tool for the visualization of splicing events across multiple samples
LuChenLab/hemato
Short-read and long-read RNA sequencing of mouse haematopoietic stem cells at bulk and single-cell levels
LuChenLab/MA-ARDS
LuChenLab/MeDAS
MeDAS: a Metazoan Developmental Alternative Splicing database
LuChenLab/RNA_Seq_protocol
RNA-Seq protocol of HISAT2-StringTie-Ballgown
LuChenLab/scrna
LuChenLab/AANanopore
LuChenLab/AANanoporeR
LuChenLab/Malarialipidmetabolism
LuChenLab/Map4k4
Map4k4 regulates neutrophil differentiation through phosphorylation of apoptotic genes
LuChenLab/scATS
Single cell ATS
LuChenLab/SPaISO-Seq
LuChenLab/T_cells_stemness
LuChenLab/FAScore
LuChenLab/MRGI
LuChenLab/r-scATS
An R package for quantifying alternative transcription start site (ATS) in 5' single-cell RNA-seq data
LuChenLab/Rscript_for_BeadChip
LuChenLab/UCB_Splicing
LuChenLab/vcfscripts
This is a bash shell script for genotypes outputting through vcf files based on 1000 Genomes Project using VCFtools.