|
| Status |
Public on Aug 07, 2012 |
| Title |
HEK293 4SU nuclear RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 4SU nuclear RNA-seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
|
| Treatment protocol |
HEK293 cells were incubated with 4-thiouridine over night
|
| Growth protocol |
HEK293 cells were cultured in DMEM medium with 10% FBS at 37°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei were extracted from cells treated with 4SU overnight. Nuclear RNA was extracted using TRIzol (Invitrogen) and reverse transcribed using random hexamer, and sequenced using Illumina Hi-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
quality filtering according to the Illumina quality filter
Bowtie alignment using the following parameter setting:--best --chunkmbs 512 -S -M 100 -p 8 -k 1
Aligned reads were used to compute the relative substitution frequency at positions with coverage of at least 20
Genome_build: hg19
Supplementary_files_format_and_content: The final file contains information about read substitutions with respect to the reference genome at specific genomic positions. Each row specificies one substitution. The columns contain information regarding chromosome, genomic position (zero offset), strand, substitution, coverage at position and number of specified substitions at the position
|
| |
|
| Submission date |
Apr 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Cem Sievers |
| E-mail(s) |
cem.sievers@bsse.ethz.ch
|
| Organization name |
ETH Zurich
|
| Street address |
Mattenstrasse
|
| City |
Basel |
| ZIP/Postal code |
4057 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE37524 |
Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data |
|
| Relations |
| SRA |
SRX144164 |
| BioSample |
SAMN00862541 |
