|Public on Jul 11, 2016
|Neural progenitor cells_ELAVL2_GFP
|tissue source: mid-gestation fetal brain
cell type: primary human neural progenitor cells
transfected with: control shRNA
genotype/variation: GFP control
time point: differentiated into neurons for 4 weeks and then harvested
|RNA was extracted after three days post-transduction using Qiagen’s miRNeasy Kit according to the manufacturer’s instructions.
|Differentiated human neural progenitors were used
|All RNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer (Agilent). Samples were randomized for RNA extractions and sequencing. 1ug of total RNA were treated with Ribo-zero Removal Kit according to the manufacturer’s instructions to remove ribosomal RNA.
Libraries were prepared using an Illumina TruSeq kit according to the manufacturer’s instructions.
|Illumina HiSeq 2500
|Single-end unstranded reads were aligned in a staged manner. Reads were aligned with segemehl using default options to a reference sequence comprised of mitochondrial DNA (h19/GRCh37 from Ensembl).
RNA-seq Counts values were quantified using R and confirmed by Htseq-Count, providing transcript database and gtf file related to GRCh37 from Ensembl.
RNA-seq RPKM values were then quantified using R.
Gene counts were used for differentially expression. Gene-level RPKMs quantifications were used for the remaining downstream processing.
Genome_build: Human h19/GRCh37 from Ensembl
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample.
|May 20, 2015
|Last update date
|May 15, 2019
|UT Southwestern Medical Center
|5323 Harry Hines Blvd.
|ELAVL2-regulated transcriptional networks in human neurons link atlernative splicing, autism and human neocortical evolution