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Sample GSM4306618 Query DataSets for GSM4306618
Status Public on Feb 12, 2020
Title Sample_NC_1
Sample type SRA
 
Source name Stomach adenocarcinoma
Organism Homo sapiens
Characteristics cell line: SGC-7901 cell
knockdown: wild type
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 SAMN14083511
SRA SRX7708123

Supplementary file Size Download File type/resource
GSM4306618_Sample_NC_1_AS_result.xlsx 3.3 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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