|
| Status |
Public on Feb 01, 2015 |
| Title |
Pol II-CLIP |
| Sample type |
SRA |
| |
|
| Source name |
hela cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: epithelial
passages: 10 to 12
clip antibody: Pol II (Abcam, cat# ab5095)
cell line: HeLa
|
| Treatment protocol |
pre-treated with 20 μg/ml α-Amanitin
|
| Growth protocol |
DMEM with 10%FBS grows in 37℃，5%CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
CLIP-seq
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
clean reads after getting rid of the adapto
All steps were referred to the method in "Circular RNAs are a large class of animal RNAs with regulatory potency"
Illumina Casava1.7 software used for basecalling.
CLIP-seq reads were aligned to hg19 genome using bowtie2 to get the unmaped reads
Data were filtered using the following specifications
Align the unmaped reads again to get the circular exon-exon junction reads and the information of the circular RNAs
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include circular RNA information for each Sample
|
| |
|
| Submission date |
Dec 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ge Shan |
| E-mail(s) |
wyc815@mail.ustc.edu.cn
|
| Phone |
86-551-63606274
|
| Organization name |
University of Science and Technology of China
|
| Department |
School of Life Sciences
|
| Street address |
443 Huangshan Road
|
| City |
Hefei |
| State/province |
Anhui |
| ZIP/Postal code |
230027 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE64443 |
Exon-Intron circular RNAs regulate transcription in the nucleus |
|
| Relations |
| BioSample |
SAMN03272445 |
| SRA |
SRX821597 |
