|
| Status |
Public on Nov 07, 2022 |
| Title |
DAP5-2_Ribo: DAP5-null replicate 2 for Ribo-seq |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
|
| Growth protocol |
6.4x10^6 cells of HEK293T WT or DAP5-null cells were plated on 15 cm dishes 24 hrs before harvesting.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and a library prepared using the TruSeq RNA Sample Prep Kit (Illumina). For Ribo-seq, the original procedure of Ingolia et al (2012) Nature Protocols was followed with modifications from Calviello et al (2016) Nature Methods.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Library strategy: Ribo-Seq
Illumina software used for basecalling.
Adapters removed with Flexbar, ribosomal-derived reads were removed using Bowtie2
Remaining reads were then mapped on hg19 using Tophat2
Ribo-seq reads were analyzed for three-nucleotide periodicity using the RiboTaper
Read count analysis was done with an R/Bioconductor package QuasR
Differential gene expression analysis with an R/Bioconductor package edgeR
Translation efficiency (TE) was estimated using the statistical framework and analysis as implemented in the RiboDiff program
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file for readcounts; tab-delimited file for differential expression analysis; tab-delimited file for translation efficiency analysis
|
| |
|
| Submission date |
Aug 07, 2020 |
| Last update date |
Nov 07, 2022 |
| Contact name |
Ramona Weber |
| E-mail(s) |
ramona.weber@uzh.ch
|
| Organization name |
University of Zurich
|
| Department |
Institute for Regenerative Medicine
|
| Street address |
Wagistrasse 12
|
| City |
Schlieren |
| ZIP/Postal code |
8952 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE155854 |
DAP5 enables main ORF translation on mRNAs with structured and uORF-containing 5’ leaders |
|
| Relations |
| BioSample |
SAMN15756317 |
| SRA |
SRX8905249 |
