|Public on Jan 06, 2017
|Nat1-/- C3 RPF rep3
|C3, Nat1-null mouse embryonic stem cell line, LIF, RPF
cell type: mouse embryonic stem cell line
|Mouse embryonic stem cells were treated with LIF.
|Standard mouse ESC medium on gelatin-coated plates at 37 ºC in a humidified incubator with 5% CO2.
|RNA was extracted using the TruSeq Ribo Profile Mammalian Kit (Illumina) according to the manufacturer's instruction.
Libraries were prepared using the TruSeq Ribo Profile Mammalian Kit (Illumina) according to the manufacturer's instruction.
|Illumina NextSeq 500
Nat1-null mouse embryonic stem cells cultured with LIF, replicate 3.
Processed data file: NormalizedCounts.txt
|Library strategy: Ribo-Seq
Fastq files were generated with bcl2fastq v2.17 (Illumina). Bases with low quality scores and the adapters in all the sequenced reads were trimmed with cutadapt-1.9.1. The trimmed reads were mapped to mouse rRNA and tRNA sequences with Bowtie2 version 2.2.8, and the reads aligned to rRNA or tRNA were excluded from further analysis. The remaining reads were mapped to mouse genome (mm10) using tophat-2.1.0 with GENECODE annotation (GRCm38.p4, Release M10). The number of reads mapped to each gene was counted by HTSeq-0.6.1 software and normalized with the DESeq2 R/Bioconductor package (v. 1.10.1) for RPF and total RNA independently.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: NormalizedCounts.txt: Tab-delimited text file contains the normalized counts data.
|Oct 20, 2016
|Last update date
|May 15, 2019
|Center for iPS Cell Research and Applicaton (CiRA), Kyoto University
|53 Kawahara-machi, Shogoin, Sakyo-ku
|Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells [ribosome profiling]
|Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells