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Sample GSM3396267 Query DataSets for GSM3396267
Status Public on Sep 30, 2019
Title A4_EBs Day 4_BPA
Sample type SRA
 
Source name EBs Day 4 treated with BPA
Organism Mus musculus
Characteristics strain: 129S4/SvJae
cell type: J1-derived EBs
day of differentiation: 4
treatment: BPA
Extracted molecule total RNA
Extraction protocol RNA was extracted with Trizol and further purified with a Qiagen Rneasy Plus kit
RNA libraries were prepared for sequencing using standard protocols at BGI
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Data processing Base-calling was performed with the BGISEQ-500 software, version 0.3.8.1111
Raw reads were subjected to quality control, filtered into clean reads and aligned to the reference sequences with Bowtie2 (parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200) and HISAT (parameters: -p 8 --phred64 --sensitive -I 1 -X 1000).
Gene quantification was performed with RSEM and expression levels calculated with the FPKM method.
To identify DEGs, FDR ≤ 0.001 and the absolute value of Log2Ratio ≥ 1' were used as default thresholds to judge the significance of gene expression difference.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each sample
 
Submission date Sep 20, 2018
Last update date Oct 01, 2019
Contact name Francesco Faiola
E-mail(s) faiola@rcees.ac.cn
Organization name Research Center foe Eco-Environmental Sciences, Chinese Academy of Sciences
Street address 18 Shuangqing rd
City Beijing
ZIP/Postal code 100085
Country China
 
Platform ID GPL23479
Series (1)
GSE120224 Effects of BPA, BPF and BPS treatments on mESC EB-based global and neural differentiations.
Relations
BioSample SAMN10095322
SRA SRX4720072

Supplementary file Size Download File type/resource
GSM3396267_A4.gene.FPKM.txt.gz 255.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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