|
| Status |
Public on Jul 11, 2016 |
| Title |
ELAVL2_GFP3 |
| Sample type |
SRA |
| |
|
| Source name |
Neural progenitor cells_ELAVL2_GFP
|
| Organism |
Homo sapiens |
| Characteristics |
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
|
| 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 |
SAMN03703110 |
| SRA |
SRX1034547 |
