|
| Status |
Public on Jun 01, 2012 |
| Title |
RNAseq_4SU+6SG_noUV |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 cell culture
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: 4SU+6SG labeling and no UV
purification: oligo(dT)
|
| Treatment protocol |
HEK293 cells were metabolically labeled with 4-thiourdine (4SU) anat a final concentration of 200 μM and 6-thioguanosine (6SG) at a final concentration of 200 μM and UV-crosslinked at 365 nm or untreated. mRNA was purified by oligo(dT) precipitation. . To monitor the incorporation of photoreactive nucleotides into mRNA, we isolated 4SU- and 6SG-labeled RNA from the oligo(dT) precipitate of non-crosslinked cells by biotinylation and streptavidin purification (Dolken et al., 2008).
|
| Growth protocol |
HEK293 cells were grown in DMEM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Illumina RNAseq protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
We computed transcript abundance estimates (FPKM values) using cufflinks (version 1.03; (Trapnell et al., 2010)) with options --frag-bias-correct and --multi-read-correct.
Genome_build: hg18
Supplementary_files_format_and_content: .csv files contains FPKM values
|
| |
|
| Submission date |
May 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Markus Landthaler |
| E-mail(s) |
markus.landthaler@mdc-berlin.de
|
| Phone |
+49-30-9406-3026
|
| Organization name |
Max-Delbrück-Center for Molecular Medicine
|
| Department |
Berlin Institute for Medical Systems Biology
|
| Street address |
Robert-Rössle-Straße 10
|
| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE38157 |
The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts |
| GSE38356 |
The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [RNA-seq] |
|
| Relations |
| SRA |
SRX149163 |
| BioSample |
SAMN00997838 |
