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Sample GSM2643099 Query DataSets for GSM2643099
Status Public on Jan 01, 2019
Title EpiLC_cyt_rep3
Sample type SRA
 
Source name EpiLC, cytoplasmic
Organism Mus musculus
Characteristics originating cell line: E14
cell type: EpiLC
subcellular fraction: cytoplasmic
Treatment protocol Cellular fractionation was prepared as described (Pandya-Jones and Black, 2009), with minor changes. 1x10e7 cells (E14) were gently trypsinized from plate and centrifugation. As for isolation of nuclei, the lysate was layered on to 500 ul cold sucrose buffer.
Growth protocol mESCs (E14) were cultured in serum-free N2B27 medium containing 2i (MEK and GSK inhibitor, PD0325901 and CHIR99021) and LIF. The nESC-to-EpiLC transition was conducted as described (Hayashi et al., 2011) with minor modifications. Briefly, mouse nESCs cells were plated at a density of 1x10e4 per cm2 in gelatin-coated plates with N2B27 medium containing activin A (20 ng/ml) and bFGF (12 ng/ml). The medium was changed every day. The converted EpiLCs were collected at day 3.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared with TRIzol reagents (Life Technologies).
Ribosomal RNA depleted and strand-specific libraries were constructed with the Ribo-zero gold (Epicentre) and TruSeq Stranded Total RNA Sample Prep kit (Illumina), and the libraries were sequenced using the HiSeq system (lllumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description EPI_cyt_3_0
Processed data file: EPI_genes.fpkm_table.txt
Data processing Illumina Casava1.7 software used for basecalling.
We trimmed and mapped reads to the mouse mm10 reference assembly (GRCm38) by the Tophat2 software (Kim et al., 2013). We used default parameters except that we reduced maximum insertion and deletion length to 2bp, and kept only uniquely mapping, “no mixed” and “no discordant” reads.
We quantified gene expression levels in each sample by cuffnorm (Trapnell et al., 2012) with default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_genes.fpkm_table.txt: Tab-delimited text files include FPKM values for each replicate.
 
Submission date May 26, 2017
Last update date May 15, 2019
Contact name Bo Wen
E-mail(s) bowen75@fudan.edu.cn
Organization name Fudan University
Department Institutes of Biomedical Sciences
Street address 130 DongAn Road
City Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL21493
Series (1)
GSE99366 RNA-seq of subcellular fractions from nESC and EpiLC
Relations
BioSample SAMN07172879
SRA SRX2863236

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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