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Jennifer VanOudenhove at
UCONN HEALTH
built this track, and the
Cotney Lab
is responsible for its contents.
Methods Description
Human embryonic heart tissue was collected, staged and provided by the
Joint MRC/Wellcome Trust Human Developmental Biology Resource.
Each embryon is identified by stage_ID. Tissues were flash frozen upon collection and stored at -80C.
RNA was extracted using miRNeasy RNA extraction kit with on-column DNAse treatment according to the manufacturer’s protocol (Qiagen). RNA integrity was checked using Agilent Tapestation 2200. RNA-seq libraries were prepared from 100-200ng total RNA using the TruSeq stranded mRNA kit (Illumina).
RNA-Seq Data Analysis
RNA-seq libraries were sequenced using the NextSeq (Illumina). Fastq files were demultiplexed by barcode yielding Fastq files for each tissue replicate.
Trimming for adapters, quality and length was performed using Trimmomatic (v.0.36). Trimmed fastqs were aligned with Rail-RNA
(Nellore et al., 2017), using human assembly GRCh38/hg38.
References
Nellore, A., Collado-Torres, L., Jaffe, A.E., Alquicira-Hernandez, J., Wilks, C., Pritt, J., Morton, J., Leek, J.T., and Langmead, B. (2017). Rail-RNA: scalable analysis of RNA-seq splicing and coverage. Bioinformatics 33, 4033–4040.
Contacts
Please email Jennifer VanOudenhove or Justin Cotney for questions.
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