|
| Status |
Public on Dec 11, 2015 |
| Title |
Elp3cKO_ribo_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Forebrains
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: E14.5 mouse embryos
genotype/variation: Elp3cKO
replicate: 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen tissues were homogenized in20 mM Tris (pH=7.5), 150 mM NaCl, 5 mM MgCl2, 1% Triton X100, 1 mM DTT, 100 µg/mL cycloheximide, 25 U/mL Turbo DNase (Ambion). RNase-treated extracts were resolved on sucrose gradients, and RNA from monosome fractions was extracted by hot phenol. Ribosome footprints of 28-32 nt were purified by size selection and gel extraction.
Footprints were dephosphorylated and ligated to a preadenylated 3' linker. Following reverse transcription, cDNA was circularized and amplified by PCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
Basecalls were performed with Illumina Casava 1.8.
The FastX-toolkit was used to remove 3' adapter sequences.
Reads were aligned to rRNA genes with Bowtie 1.0.0. Non-rRNA reads were mapped with Bowtie to reference sets consisting of UCSC canonical genes containing 18 nt of genomic flanking regions. Only reads with unique matches to the sense strand and a maximum of one mismatch in the seed sequence were retained for further analysis.
Raw read counts were determined using custom scripts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing gene annotations and raw read count data.
|
| |
|
| Submission date |
Nov 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Danny D. Nedialkova |
| E-mail(s) |
danny.nedialkova@mpi-muenster.mpg.de
|
| Organization name |
Max Planck Institute for Molecular Biomedicine
|
| Department |
Max Planck Research Group for RNA Biology
|
| Street address |
Von-Esmarch-Str. 54
|
| City |
Münster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16173 |
| Series (1) |
| GSE74683 |
A dynamic unfolded protein response contributes to the control of cortical neurogenesis |
|
| Relations |
| BioSample |
SAMN04240482 |
| SRA |
SRX1418180 |
