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Sample GSM1064936 Query DataSets for GSM1064936
Status Public on Aug 30, 2013
Title Vehicle_RNAseq_rep4 [mouse]
Sample type SRA
Source name cultured cortical neurons
Organism Mus musculus
Characteristics strain: C57BL/6J x CASTEi/J
age: 10 days in vitro
cell type: cultured cortical neurons
agent: Vehicle
Treatment protocol After 7 days in vitro, neurons were treated with 300 nM topotecan or vehicle. After 72 hrs drug treatement, cells were harvested for RNAseq or ChIPseq.
Growth protocol Cortical neurons were cultured from E13-15 mouse embryos for 7 days in vitro.
Extracted molecule polyA RNA
Extraction protocol RNA was extracted using Trizol reagent.
Libraries were constructed with Illumina TruSeq kits for RNA or ChIPseq.
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 mm9 genome using bowtie version 0.12.7 with default parameters for RNA-seq, m-1 was used for Chip-seq mapping
Traveling ratios (TR) were calculated after removing duplicate reads, as the ratios between reads mapped (Reads per million) to promoter region and the gene body.
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: mm9
Supplementary_files_format_and_content: ChIP-Seq: Tab-delimited text files containing traveling ratio for each sample.
Supplementary_files_format_and_content: RNA-Seq: Tab-delimited text files containing RPKM values for each sample.
Submission date Jan 16, 2013
Last update date May 15, 2019
Contact name Chandri Yandava
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 GPL13112
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
Reanalyzed by GSE80797
SRA SRX217728
BioSample SAMN01888174

Supplementary file Size Download File type/resource
GSM1064936_Vehicle11_RPKM.txt.gz 133.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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