|
| Status |
Public on Jan 10, 2023 |
| Title |
CHO K1 dph2, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
CHO K1 cell line
|
| Organism |
Cricetulus griseus |
| Characteristics |
tissue: Ovary
genotype: dph2
cell line: CHO K1 [ATCC CCL-61]
treatment: No treatment
agent: cycloheximide
|
| Treatment protocol |
Refer to SAMPLES treatment columns
|
| Growth protocol |
Yeast cells were grown to A600 0.6-1.0 in selective media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Yeast cells were lysed by grinding by Freezer Mill. CHO cells were lysed by lysis buffer containing Triton X-100. Ribosomes were collected by sucrose cushion with ultracentrifugation. RNAs were extract by Direct-zol RNA Microprep Kits.
Libraries were prepared according to published protocol by Ingolia (Methods 2017)
Ribosome protected fragments (riboseq)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Library strategy: Ribo-Seq
Sequencing data were provided by NHLBI DNA Sequencing and Genomics Core (NIH)
Linker was removed by cutadapt 2.8 with Python 3.7.5
After sorting the sequences by sample barcodes, PCR duplicates were removed by custom Python script.
rRNAs, tRNAs and other non-coding RNAs were removed by bowtie 1.1.2.
Alignments were done by bowtie 1.1.2 with the option -v 2 -m 1 -a -y --best --strata
Genome_build: Yeast trascriptome of R64-1-1 S288C reference genome assembly (SacCer3) was used. 3' and 5' UTR information was from Pelechano and Steinmetz (Nature 2013) and modified by Ingolia.
|
| |
|
| Submission date |
Jun 04, 2021 |
| Last update date |
Jan 11, 2023 |
| Contact name |
Byung-Sik Shin |
| E-mail(s) |
[email protected]
|
| Phone |
2404831725
|
| Organization name |
NIH
|
| Lab |
Protein Biosynthesis
|
| Street address |
6 Center Dr, BLDG 6, RM 227
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL27425 |
| Series (1) |
| GSE176169 |
Role of eEF2 diphthamide modification in translational fidelity |
|
| Relations |
| BioSample |
SAMN19572233 |
| SRA |
SRX11070662 |
