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Sample GSM1692714 Query DataSets for GSM1692714
Status Public on Jul 11, 2016
Title ELAVL2_1
Sample type SRA
 
Source name Neural progenitor cells_ELAVL2
Organism Homo sapiens
Characteristics tissue source: mid-gestation fetal brain
cell type: primary human neural progenitor cells
transfected with: shRNA targeting ELAVL2
genotype/variation: ELAVL2 knockdown
time point: differentiated into neurons for 4 weeks and then harvested
Treatment protocol RNA was extracted after three days post-transduction using Qiagen’s miRNeasy Kit according to the manufacturer’s instructions.
Growth protocol Differentiated human neural progenitors were used
Extracted molecule total RNA
Extraction protocol 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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing 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.
 
Submission date May 20, 2015
Last update date May 15, 2019
Contact name Genevieve Konopka
E-mail(s) gena@alum.mit.edu
Organization name UT Southwestern Medical Center
Department Neuroscience
Street address 5323 Harry Hines Blvd.
City Dallas
State/province TX
ZIP/Postal code 75390-9111
Country USA
 
Platform ID GPL16791
Series (1)
GSE69092 ELAVL2-regulated transcriptional networks in human neurons link atlernative splicing, autism and human neocortical evolution
Relations
BioSample SAMN03703103
SRA SRX1034540

Supplementary file Size Download File type/resource
GSM1692714_EL-1_RPKM.txt.gz 490.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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