Computational protocol: Lsh/HELLS regulates self-renewal/proliferation of neural stem/progenitor cells

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Protocol publication

[…] Total RNA from NSPCs passage 2 was used for mRNA isolation and cDNA library construction with the TruSeq RNA Sample Preparation Kit (Illumina). Clusters were generated with the TruSeq PE Cluster Kit v3-HS & TruSeq SBS kit v3-HS according to the reagent preparation guide. The RNA sequencing was performed using the Illumina HiSeq2500. High quality 100 bp reads were aligned to the mouse reference genome (mm9) using TopHat 2.0.8. The expression levels for each of the genes were normalized to reads per kb of exon model per million mapped reads (RPKM) to compared mRNA levels between samples. Differentially expressed genes were identified by Cuffdiff form Cufflinks 2.2.0 with default parameters. […]

Pipeline specifications

Software tools TopHat, Cufflinks
Application RNA-seq analysis
Organisms Homo sapiens, Mus musculus
Diseases Congenital Abnormalities, Immunologic Deficiency Syndromes, Nervous System Diseases