|
| Status |
Public on May 23, 2017 |
| Title |
KO3_mRNA |
| Sample type |
SRA |
| |
|
| Source name |
HAP-1 EEF1AKMT4_RNA-seq
|
| Organism |
Homo sapiens |
| Characteristics |
commercial name: Horizon Genomics, HZGHC000530c015
cell line: HAP-1
genotype: EEF1AKMT4 KO
|
| 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 |
RNASeq libraries were prepared from cells lysed similar to ribosome profiling samples. RNA was isolated from cleared lysates by addition of 1 % SDS (w/v) and 5 min incubation at 65 °C with intermittent vortexing followed by three rounds of extraction using 10:1 acid-phenol pH 4.3 and bromochloropropane.
Total RNA was precipitated and 5 µg used for library generation with the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions. Libraries were sequenced on an Illumina HiScanSQ generating 50 nt single-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
mRNA
|
| Data processing |
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 |
| BioSample |
SAMN06648046 |
| SRA |
SRX2677578 |
