|
| Status |
Public on Aug 30, 2013 |
| Title |
Vehicle_RNAseq [human] |
| Sample type |
SRA |
| |
|
| Source name |
iPSCs were differentiated into forebrain cortical neurons and treated with vehicle for 6 days.
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: forebrain cortical neurons
agent: Vehicle
|
| Treatment protocol |
iPSCs were differentiated into forebrain cortical neurons and treated with 10µM topotecan or vehicle for 6 days.
|
| Growth protocol |
iPSCs derived from an Angelman Syndrome patient were cultured on irradiated mouse embryonic fibroblasts as described in Chamberlain et al. (PMID 20876107)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using Trizol reagent.
Sranded libraries were constructed with Illumina kits for Stranded RNAseq.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using Illumina CASAVA version 1.3 for single-end reads and CASAVA version 1.8 for paired-end reads
Reads were mapped to hg19 genome using bowtie version 0.12.7 with default parameters for RNA-seq
Reads Per Kilobase of exon per million of reads mapped (RPKM) were calculated using R package DEGSeq (Wang et al., Bioinformatics, 2010) for RNA-seq
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing RPKM values for each sample.
|
| |
|
| Submission date |
Jul 02, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Chandri Yandava |
| E-mail(s) |
yandava@email.unc.edu
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Carolina Institute for Developmental Disabilities
|
| Street address |
101 Renee Lynne Court
|
| City |
Carrboro |
| State/province |
NC |
| ZIP/Postal code |
27510 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE43526 |
Co-ordinate inhibition of autism candidate genes by topoisomerase inhibitors [Seq] |
| GSE43900 |
Co-ordinate inhibition of autism candidate genes by topoisomerase inhibitors |
|
| Relations |
| BioSample |
SAMN02223075 |
| SRA |
SRX317225 |
