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Sample GSM2357216 Query DataSets for GSM2357216
Status Public on Jan 06, 2017
Title Nat1+/- A7 RPF rep1
Sample type SRA
 
Source name A7, Nat1 heterozygous mouse embryonic stem cell line, LIF, RPF
Organism Mus musculus
Characteristics genotype/variation: Nat1 heterozygous
cell type: mouse embryonic stem cell line
treatment: LIF
Treatment protocol Mouse embryonic stem cells were treated with LIF.
Growth protocol Standard mouse ESC medium on gelatin-coated plates at 37 ÂșC in a humidified incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol 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.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description A7_RPF
Nat1 heterozygous mouse embryonic stem cells cultured with LIF, replicate 1.
RPF
Processed data file: NormalizedCounts.txt
Data processing 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.
 
Submission date Oct 20, 2016
Last update date May 15, 2019
Contact name Shinya Yamanaka
E-mail(s) yamanaka@cira.kyoto-u.ac.jp
Phone 81-75-366-7041
Organization name Center for iPS Cell Research and Applicaton (CiRA), Kyoto University
Street address 53 Kawahara-machi, Shogoin, Sakyo-ku
City Kyoto
ZIP/Postal code 606-8507
Country Japan
 
Platform ID GPL19057
Series (2)
GSE89011 Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells [ribosome profiling]
GSE89012 Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells
Relations
BioSample SAMN05931403
SRA SRX2255514

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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