|
| Status |
Public on Sep 24, 2019 |
| Title |
EBO3_mut_14 |
| Sample type |
SRA |
| |
|
| Source name |
cell culture
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: RPS2 A226Y
cell line: HEK293
|
| Growth protocol |
HEK293 cells stably transfected with RPS2 wild-type or RPS2 A226Y mutant expressing constructs were cultured in Dulbecco's MEM medium supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cell culture samples was isolated using RNeasy Mini Kit (Qiagen). Total RNA from muscle samples was isolated using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA 1.8 and convered into fastq files with bcl2fastq-1.8.4
RNA-Seq reads were aligned to Ensembl GRCh37 genome assembly using STAR_2.4.2a with following parameters: --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Counts were generated with the function featureCounts in the Rsubreads package.
Genome_build: GRCh37
Supplementary_files_format_and_content: count file was generated with the function featureCounts in the Rsubreads package. The numbers are raw counts.
|
| |
|
| Submission date |
May 31, 2018 |
| Last update date |
Sep 24, 2019 |
| Contact name |
Youjin Teo |
| E-mail(s) |
youjin.teo@uzh.ch
|
| Phone |
+41792588406
|
| Organization name |
Universität Zürich
|
| Department |
Institut für Medizinische Mikrobiologie
|
| Lab |
Erik C. Böttger
|
| Street address |
Gloriastrasse 30
|
| City |
Zürich |
| ZIP/Postal code |
8006 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE115153 |
Biological effect of chronic mistranslation in mammalian cells |
|
| Relations |
| BioSample |
SAMN09288614 |
| SRA |
SRX4147564 |
