Computational protocol: Interplay between H1 and HMGN epigenetically regulates OLIG1&2 expression and oligodendrocyte differentiation

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Protocol publication

[…] Total RNA from ESCs or embryoid bodies was isolated by RNeasy Mini Kit (Qiagen) followed by ‘on-column’ DNase I treatment. mRNA-seq libraries were prepared from 1 μg of total RNA using the Illumina TruSeq RNA Sample Preparation Kit, following the manufacturer's instructions. Libraries were sequenced on the Illumina HiSeq 2000 with 2 × 100 bp paired-end reads. The data analysis was performed using the RNA-seq pipeline in Partek Genome Suite. A gene was considered expressed if reads per kilobase of transcript model per million mapped reads (RPKM) was ≥1.0. |Fold Change| ≥ 1.5 with P-value <0.05 was considered significantly differentially expressed between WT and DKO. Gene ontology analysis was performed using DAVID online software (https://david.ncifcrf.gov/). Genomatix Pathway System (GePS, Genomatix GmbH) was used to generate a simple network using the following criteria: organism—Mus musculus; annotation type—biological processes; subcategory—nervous system development. […]

Pipeline specifications

Software tools DAVID, GePS
Application RNA-seq analysis
Organisms Mus musculus