|
| Status |
Public on Aug 26, 2022 |
| Title |
Ribosome_profiling_Control_siRNA_1.fastq.gz |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Control for Ribosomal profiling plus Harringtonine
|
| Treatment protocol |
Libraries from cultured cells were prepared as described previously (Loayza-Puch et al., 2013), with an addition of harringtonine treatment for 5 minutes that added to the cell culture medium (final concentration of 2 µg/ml -Santa Cruz sc-204771A) prior to CHX treatment.
|
| Growth protocol |
HeLa, U2OS, HEK293 and MEF cell lines were grown in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal calf serum, 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C. Cell lines were regularly tested for Mycoplasma contamination. Cell lines were authenticated by expression analysis based on RNA-seq.
|
| Extracted molecule |
other |
| Extraction protocol |
Libraries from cultured cells were prepared as described previously (Loayza-Puch et al., 2013), with an addition of harringtonine treatment for 5 minutes that added to the cell culture medium (final concentration of 2 µg/ml -Santa Cruz sc-204771A) prior to CHX treatment.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
For the Ribosome profiling analysis, reads in FASTQ format were trimmed for adapters using cutadapt, and were aligned to human hg19 trancriptome (gencode v19) using bowtie. Samtools (Li et al., 2009) and bedtools (Quinlan and Hall, 2010) were used for file format conversion (SAM to BAM and BAM to BED). Finally, CDS alignment was retained using PERL script which was covered into tabular format using custom PERL script, generating read count data for every one of the hundred windows covering the length of transcript, generated using BEDTOOLS. Peaks were identified with a custom R script using the findPeaks function from the package PRACMA. The fraction of reads for every peak identified in a transcript were identified by percentile normalization. Processed data files Ribosome_htseq_readcounts.txt is a tab delimited .txt files containing raw read counts obtained from HTSEQ (0.5.4p3) at exons of genes. Ribosome_profiling_Control_siRNA_1.bw is a bigwig file
|
| |
|
| Submission date |
Apr 23, 2020 |
| Last update date |
Aug 26, 2022 |
| Contact name |
Pierre-Rene Körner |
| Organization name |
Netherlands Cancer Institute (NKI)
|
| Department |
Oncogenomics
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE149204 |
Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential |
|
| Relations |
| BioSample |
SAMN14678269 |
| SRA |
SRX8163581 |
