 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 02, 2019 |
| Title |
D12100 |
| Sample type |
SRA |
| |
|
| Source name |
Embryoid body
|
| Organism |
Mus musculus |
| Characteristics |
cell line: J1
cell type: mESC
treatment: 100 nM TBBPA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent and purified with RNeasy Plus mini Kit
The procedures were performed at Beijing Genomics Institute (BGI), Wuhan, China. RNA samples were analyzed with a 2100 Bioanalyzer (Agilent Technologies, USA), and subjected to library preparation according to BGI standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Sequencing was performed with a BGISEQ-500 platform and generated 21,761,200 raw sequencing reads. Clean reads (21,628,715) were mapped to the reference genome (GCF_000001635.25_GRCm38.p5) using HISAT/Bowtie2 with a mean mapping rate of 86.03%.
The fragments per kilobase of exon per million fragments mapped (FPKM) method was used to calculated gene expression levels.
Differentially expressed genes (DEGs) were defined as log2-Ratio ≥ 1 and q-value (corrected p-value) £ 0.001.
Genome_build: GCF_000001635.25_GRCm38.p5
Supplementary_files_format_and_content: Text file and FPKM values for all samples
|
| |
|
| Submission date |
Jan 18, 2019 |
| Last update date |
Dec 02, 2019 |
| Contact name |
Shaojun Liang |
| E-mail(s) |
liangshaojun1989@126.com
|
| Organization name |
Chinese academy of sciences
|
| Street address |
18 Shuangqing Road
|
| City |
Beijing |
| ZIP/Postal code |
100085 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE125324 |
Embryoid Body-based RNA-seq Analyses Reveal a Potential TBPPA Multifaceted Developmental Toxicity |
|
| Relations |
| BioSample |
SAMN10769721 |
| SRA |
SRX5261299 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3568953_D12100.gene.fpkm.txt.gz |
3.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
