|
| Status |
Public on Apr 24, 2015 |
| Title |
SH-SY5Y exp1 day 4 |
| Sample type |
SRA |
| |
|
| Source name |
SH-SY5Y cells; CRL-2266 (ATCC)
|
| Organism |
Homo sapiens |
| Characteristics |
differentiation stage: day 4 after retinoic acid treatment
|
| Treatment protocol |
retinoic acid induction; 1µM in neurobasal medium, 1X B27
|
| Growth protocol |
DMEM/F12 supplemented with L-glutamine and non-essential amino-acids, 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIZOL
Ribodepletion followed by default Illumina RNA-Seq for HiSeq2000 (TruSeq)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
day 4 after retinoic acid treatment
genome build: hg19
|
| Data processing |
Illumina base calling, demultiplexing, and FASTQ conversion with CASAVA-1.8.2
alignment genome reference using bowtie2
20nt anchors from both ends of unaligned reads aligned to genome independently
aligned anchors were extended to find circRNA head-to-tail splice sites (see Suppl. Methods)
Supplementary_files_format_and_content: bed file; circRNA head-to-tail splice sites with number of supporting reads in the score column
|
| |
|
| Submission date |
Apr 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Petar Glazar |
| Organization name |
Max Delbrück Center for Molecular Medicine
|
| Department |
Systems Biology of Gene Regulatory Elements
|
| Lab |
Rajewsky lab
|
| Street address |
Robert Rössle Str. 10 (H. 87)
|
| City |
Berlin |
| ZIP/Postal code |
13092 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE65926 |
Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed |
|
| Relations |
| BioSample |
SAMN03566487 |
| SRA |
SRX1007601 |
