|
| Status |
Public on Apr 12, 2016 |
| Title |
Ribo-Seq (MEF cells, mutant 18S rRNA) |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Embryonc Fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell line: MEF
tissue: Embryonc Fibroblasts
|
| Treatment protocol |
cycloheximide for 3 mins (100 ug/ml)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rnase I Digestion, RNA dephosphorylation, Size Selection
Poly-A Tailing, cDNA synthesis, Size selection, circularization, DNA precipitation, Linearization, PCR amplification
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Library strategy: Ribo-Seq
Sequencing reads were mapped to genome and NCBI refseq genes by Tophat ((--bowtie1 --no-novel-juncs -G)
P-site of RPF (13th nt) was extracted
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: wiggle file of all unique-mapping reads; ribosome occupancy file of NCBI Refseq mRNAs (according to psite of RPF)
|
| |
|
| Submission date |
Apr 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ji Wan |
| E-mail(s) |
jw896@cornell.edu
|
| Organization name |
Cornell University
|
| Street address |
303 Biotech 526 Campus Road
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE80156 |
A coding sequence-embedded principle governs translational reading frame fidelity |
|
| Relations |
| BioSample |
SAMN04632616 |
| SRA |
SRX1690317 |
| SRA |
SRX1690317 |
