|
| Status |
Public on Jan 06, 2017 |
| Title |
Nat1-/- B2 Total rep2 |
| Sample type |
SRA |
| |
|
| Source name |
B2, Nat1-null mouse embryonic stem cell line, LIF, Total RNA
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Nat1-null
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 ºC 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 |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
B2_Total
Nat1-null mouse embryonic stem cells cultured with LIF, replicate 2.
Total RNA
Processed data file: NormalizedCounts.txt
|
| Data processing |
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 |
SAMN05931412 |
| SRA |
SRX2255517 |
