|
| Status |
Public on May 23, 2017 |
| Title |
WT2_RPF |
| Sample type |
SRA |
| |
|
| Source name |
Flp-In T-REx-293 wild-type_ribosomal profiling
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Flp-In T-REx-293
genotype: wildtype
|
| Treatment protocol |
Cells were treated with 100 µg/ml cycloheximide (CHX) for 1 min, washed with ice cold PBS containing 100 µg/ml CHX and subsequently lysed in lysis buffer (10 mM Tris pH 7.5, 100 mM NaCl, 10 mM MgCl2, 1 % Triton X-100, 0.5 mM DTT, 100 µg/ml CHX).
|
| Growth protocol |
Wild type and EEF1AKMT4-deficient HAP-1 cells were cultured in IMDM GlutaMAX™, 10 % FBS and 100 U/ml penicillin-streptomycin.
|
| Extracted molecule |
polyA 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 |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
mRNA - ribosome footprints
|
| Data processing |
Library strategy: ribosome profiling
for fooprints: linkers were removed from reads using the fastx_clipper and randomized sequences removed using the fastx_trimmer (FASTX Toolkit). Already performed for uploaded files.
Data was mapped to the hg38 transcriptome (UCSC knownCanonical) with bowtie (-m 1 -v1 -l 25 --best --strata) and counts generated using a custom script.
Genome_build: hg38
Supplementary_files_format_and_content: Count table showing the raw counts of ribosome profiling and RNAseq data for detected GENCODE v24_knownCanonical transcipts (available from the UCSC table browser for hg38)
|
| |
|
| Submission date |
Mar 28, 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) |
| GSE97140 |
Methylation of human eukaryotic elongation factor alpha (eEF1A) by a member of a novel protein lysine methyltransferase family modulates mRNA translation |
|
| Relations |
| Alternative to |
GSM2445295 |
| BioSample |
SAMN06648049 |
| SRA |
SRX2677575 |
