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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 30, 2019 |
| Title |
GA9_EBs Day 9_BPA |
| Sample type |
SRA |
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| Source name |
EBs Day 9 treated with BPA
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| Organism |
Mus musculus |
| Characteristics |
strain: 129S4/SvJae
cell type: J1-derived EBs
day of differentiation: 9
treatment: BPA
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| 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
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| Submission date |
Sep 20, 2018 |
| Last update date |
Oct 01, 2019 |
| Contact name |
Francesco Faiola |
| E-mail(s) |
[email protected]
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| Organization name |
Research Center foe Eco-Environmental Sciences, Chinese Academy of Sciences
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| Street address |
18 Shuangqing rd
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| City |
Beijing |
| ZIP/Postal code |
100085 |
| Country |
China |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE120224 |
Effects of BPA, BPF and BPS treatments on mESC EB-based global and neural differentiations. |
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| Relations |
| BioSample |
SAMN10095314 |
| SRA |
SRX4720080 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3396275_GA9.gene.FPKM.txt.gz |
265.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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