Jun-Liszt Li

KITS FOR RNA EXTRACTION

      Takara: Smart-Seq

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SEQUENCING PLATFORM

         illumina: https://www.illumina.com/

         huada: 

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ANALYSIS SOFTWARES

QC:

       fastqc: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

       multiqc: https://multiqc.info/

       fastp: https://github.com/OpenGene/fastp

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Reads Mapping:

           hisat2:

           STAR:

           TopHat:

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Samtools:

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Gene Counting:

           FeatureCounts:

           HTseq-Count:

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Difference Analysis:

R packages: DESeq2:

                     edgeR:

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Single-Cell RNAseq:

R packages: Seurat: https://satijalab.org/seurat/

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Gene Symbol Converter:

https://david.ncifcrf.gov/content.jsp?file=conversion.html

https://www.syngoportal.org/convert.html

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Enrichment analysis tools

http://www.pantherdb.org/

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Genome resource

UCSC Genome Browser: http://genome.ucsc.edu/

NCBI Mouse Resources: https://www.ncbi.nlm.nih.gov/genome?term=mus%20musculus

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Gene name search:

MGI: http://www.informatics.jax.org/marker/MGI:2685385

Uniprot: https://www.uniprot.org/

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Allen Institute for Brain Science Brain Atlas: 

http://celltypes.brain-map.org/rnaseq/mouse/cortex-and-hippocampus

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Single Cell Sequencing Platforms:

10X genomics;

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Brain single-cell genomics Browsers

1. Dropviz: http://dropviz.org/

2. Mousebrain (Both adolescent and development): http://mousebrain.org/

3. VascularSingleCell: http://betsholtzlab.org/VascularSingleCells/database.html

4. Bulk RNAseq of different Brain cell types: https://www.brainrnaseq.org/

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Ref papers:

1. Sahraeian, Sayed Mohammad Ebrahim, et al. "Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis." Nature communications 8.1 (2017): https://www.nature.com/articles/s41467-017-00050-4)

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2.

3.

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Ref labs:

Single cell genomics:

Satija; NYU

Spatial Transcriptomics:

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