|
| Status |
Public on Jan 05, 2017 |
| Title |
METTL21B-2 |
| Sample type |
SRA |
| |
|
| Source name |
Flp-In T-REx-293
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: METTL21B knockout
tissue: Kidney
cell line: Flp-In T-REx-293
|
| Treatment protocol |
Cells were treated with cycloheximide for 1min, lyzed by scraping in a buffer containing 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 10 mM MgCl2, 1% Triton X-100, 0.5 mM DTT, 100 g/ml CHX and flash-frozen in liquid nitrogen.
|
| Growth protocol |
Cells were routinely cultured in Dulbecco’s modified Eagle’s medium, supplemented with 10% (v/v) fetal bovine serum (FBS), 1× GlutaMAX™ and 100 units/ml of penicillin and streptomycin (P/S).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell lysates were incubated with RNAseI and subjected to sucrose gradient centrifugation. Monosomes were isolated and used for library preparation.
Libraries were prepared by isolating ribosome prorotected fragments, 3' linker ligation, reverse transcription with an RT primer complementary to the linker, cicularization of the resulting ssDNA and a final PCR to attach illumina index primers and amplify the library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
ribosome protected RNA
|
| Data processing |
Basecalls performed using CASAVA
Adapters were clipped and reandomized nucleotides trimmed using the FASTx toolkit
Reads were aligned to human rRNA to remove rRNA derived reads and mapped to the hg19 transcriptome using bowtie
reads for each individual transcript were counted using a custom script
Genome_build: hg19
Supplementary_files_format_and_content: CSV file containing raw counts per transcript for the four different samples.
|
| |
|
| Submission date |
Jan 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Benedikt Sebastian Nilges |
| E-mail(s) |
benedikt.nilges@mpi-muenster.mpg.de
|
| Organization name |
Max Planck Institute for Molecular Biomedicine
|
| Department |
RNA Biology Group
|
| Street address |
Von-Esmarch-Straße 54
|
| City |
Muenster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15456 |
| Series (1) |
| GSE93133 |
The novel lysine specific methyltransferase METTL21B affects mRNA translation through inducible and dynamic methylation of Lys-165 in human eukaryotic elongation factor 1 alpha (eEF1A) |
|
| Relations |
| BioSample |
SAMN06203158 |
| SRA |
SRX2463230 |
