Counts: Brain transcriptome of hereditary cerebral haemorrhage with amyloidosisâ€“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.
- 36 samples
- DAC: EGAC00001000771
- Technology: Illumina HiSeq 2500
Policy: Brain Transcriptome of hereditary cerebral haemorrhage with amyloidosis–Dutch type (HCHWA-D)
Controlled access required because the study concerns linked phenotype and genotype data from human subjects which should not be traced back to the patients. Citation plus acknowledgement will be required.
Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.
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