|
| Status |
Public on Aug 30, 2013 |
| Title |
Vehicle_Chipseq [mouse] |
| Sample type |
SRA |
| |
|
| Source name |
cultured cortical neurons
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
age: 10 days in vitro
cell type: cultured cortical neurons
agent: Vehicle
antibody: Anti-PolII N20 (Santa Cruz, sc-899)
|
| 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 |
genomic DNA |
| Extraction protocol |
Cells for ChIP were fixed, nuclei isolated, and chromatin sheared by sonication. Pol2 DNA complexes were isolated by immunoprecipitation.
Libraries were constructed with Illumina TruSeq kits for RNA or ChIPseq.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| 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 |
| 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 |
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 |
|
| Relations |
| SRA |
SRX217735 |
| BioSample |
SAMN01888181 |
