Counts: Brain transcriptome of hereditary cerebral haemorrhage with amyloidosis–Dutch type (HCHWA-D)

These are the log2CPM (log2 counts per million) fragments per gene counts associated with the BAM files in EGAD00001003806, in tab separated format. Counts for 36 postmortem brain samples from 9 non-demented control subjects and 9 Hereditary cerebral hemorrhage with amyloidosis-Dutch type subjects are included (1 Frontal cortex sample and 1 Occipital cortex sample per subject). RNA samples were depleted for ribosomal RNA with the Ribo Zero Gold Human kit (Illumina) and strand specific RNA-Seq libraries were generated. Paired-end sequencing was performed on a HiSeq2500 Illumina system (2x50bp reads). Alignments were performed using GSNAP v2014-12-23 with setting "--npaths 1" on GRCh38 reference genome without the alternative contigs. Fragment per gene counting was performed using HTSeq-count v0.6.1p1 with setting "--stranded reverse". The gene annotation used for quantification were UCSC RefSeq genes for GRCh38 downloaded on 2015-07-13.EGA dataset EGAD00010001457

本数据集包含与EGAD00001003806中BAM（Binary Alignment Map）文件相关的基因水平log2CPM（log2 counts per million）片段计数数据，数据格式为制表符分隔。
本数据集涵盖9名非痴呆对照受试者与9名荷兰型遗传性淀粉样变性脑出血（Hereditary cerebral hemorrhage with amyloidosis-Dutch type）受试者的共36例死后脑组织样本的基因计数数据，每位受试者均采集1例额叶皮层样本与1例枕叶皮层样本。
RNA样本采用Illumina公司的Ribo Zero Gold Human试剂盒去除核糖体RNA，并构建了链特异性RNA-Seq文库。测序实验在Illumina HiSeq2500平台上完成，采用双端测序模式，读长为2×50bp。
序列比对步骤采用GSNAP v2014-12-23工具完成，比对参数设置为`--npaths 1`，参考基因组为去除替代contig的GRCh38版本。
基因水平的片段计数采用HTSeq-count v0.6.1p1工具完成，参数设置为`--stranded reverse`。
定量分析所用的基因注释为2015年7月13日下载的GRCh38版本UCSC RefSeq基因集，本数据集隶属于EGA数据集EGAD00010001457。