Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 9
Release date: Dec 1 2016
Last update date: Feb 26 2018
Access: Public
Diseases: Amyotrophic Lateral Sclerosis, Neurodegenerative Diseases
Genes: FUS, fus
Dataset link Characterization of genetic loss-of-function of Fus in zebrafish

Experimental Protocol


We performed paired-end sequencing (100bp reads) of the polyA+ transcriptome from brains of five individuals with Fus-/- genotype and four with Fus wild type genotype. Note on RNA-Seq replicates: after performing first RNA sequencing on four replicates of Fus-/- and WT (labeled with the prefix "Sample_imb_ketting_2014_13_") we received a notice from Illumina stating a problem with the library preparation kit lot that was used to prepare the libraries. Due to that, we performed RNA sequencing a second time, using the same input RNA, except for the Fus knockout replicate #3, because there was not enough input RNA left. Instead, a different Fus knockout replicate (#1) was sequenced. However, we compared the mapped reads from sequencing run 1 and sequencing run 2 using plotCorrelaction from DeepTools, and the samples are highly correlated (at least 0.97 and 0.95, Spearman and Pearson correlation respectively). Therefore, we considered first ("Sample_imb_ketting_2014_13_") and second sequencing runs as technical replicates.

Repositories


GEO

GSE85554

ENA

SRP081553

BioProject

PRJNA338793

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Contact


Antonio Miguel de Jesus Domingues

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