|
| Status |
Public on Feb 12, 2020 |
| Title |
Sample_sh_1 |
| Sample type |
SRA |
| |
|
| Source name |
Stomach adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SGC-7901 cell
knockdown: JMJD1A knockdown
|
| Treatment protocol |
Negative control shcontrol (NC) and shJMJD1A (sh) were transfected into cells. The transfected cells were screened with purinomycin. After screening for three times, Cell were harvested and performed to analyze JMJD1A downstream genes.
|
| Growth protocol |
Cells were cucltured in DMEM medium with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw data (raw reads) were processed using NGS QC Toolkit. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks , and the read counts of each gene were obtained by htseq-count . DEGs were identified using the DESeq (2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
If it was transcript-level quantification, FPKM and read counts value of each transcript (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using the DESeq (2012) functions estimateSizeFactors and nbinomTest. P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
The reads were reassembled using cufflinks. Then gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using cuffcompare software.
The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was performed using ASprofile.SNP and INDEL were called using samtools and bcftools, and the details were shown on samtools webpage (http://samtools.sourceforge.net/mpileup.shtml). Then snpeff annotates and predicts the effects of variants on genes (such as amino acid changes).
Genome_build: Human Ch38
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
Feb 11, 2020 |
| Last update date |
Feb 13, 2020 |
| Contact name |
Ke Ning |
| E-mail(s) |
[email protected]
|
| Organization name |
China Medial University
|
| Street address |
PuHe street No.77
|
| City |
ShenYang |
| State/province |
LiaoNing |
| ZIP/Postal code |
110122 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE145105 |
JMJD1A inhibits proliferation and aggressiveness of gastric cancer by up-regulating RUNX3 |
|
| Relations |
| BioSample |
SAMN14083508 |
| SRA |
SRX7708126 |
