Total RNA was extracted from two replicates of E16.5 mouse forebrain tissue and purified using
the RNeasy Maxi Kit (Qiagen, Venlo, Limburg, The Netherlands) and sent to Otogenetics for
ribosomal RNA depletion, cDNA production using random primers, library preparation, and pair end
sequencing (~100 bp) using Illumina HiSeq2000. Resulting reads were demultiplexed and aligned
to the mouse genome (mm9) using TopHat v2.0.7.49 (link),51 (link),52 (link) The two replicates were merged and
read counts mapping to each transcript were obtained using HTseq.53 (link) Expression of each transcript was quantified as fragments per kilobase of
transcript per million fragments mapped (FPKM) by dividing the total number of reads mapping to each
transcript by transcript length, and the total number of reads aligned to the genome divided by one
million. The Wilcoxon test from the statistical toolkit R was used to calculate differences in gene
expression between genes whose promoter contains an Auts2-marked site and all other genes. RNA-seq
data from this study are available in SRA (http://www.ncbi.nlm.nih.gov/sra ; SRR experiment SRR1298758 (replicate 1) and
SRR1298760 (replicate 2)).
the RNeasy Maxi Kit (Qiagen, Venlo, Limburg, The Netherlands) and sent to Otogenetics for
ribosomal RNA depletion, cDNA production using random primers, library preparation, and pair end
sequencing (~100 bp) using Illumina HiSeq2000. Resulting reads were demultiplexed and aligned
to the mouse genome (mm9) using TopHat v2.0.7.49 (link),51 (link),52 (link) The two replicates were merged and
read counts mapping to each transcript were obtained using HTseq.53 (link) Expression of each transcript was quantified as fragments per kilobase of
transcript per million fragments mapped (FPKM) by dividing the total number of reads mapping to each
transcript by transcript length, and the total number of reads aligned to the genome divided by one
million. The Wilcoxon test from the statistical toolkit R was used to calculate differences in gene
expression between genes whose promoter contains an Auts2-marked site and all other genes. RNA-seq
data from this study are available in SRA (
SRR1298760 (replicate 2)).
