|
| Status |
Public on Jun 12, 2024 |
| Title |
SHAP |
| Sample type |
SRA |
| |
|
| Source name |
HGC-27 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HGC-27
cell type: gastric cancer cells
treatment: SHAP
|
| Treatment protocol |
Cells were treat with control DMSO, disulfiram, thiram or SHAP peptide using RNAIMAX (Thermo) reagent for 72 hours
|
| Growth protocol |
Cells were incubated with RPMI 1640 medium with 10% FBS in CO2 incubators at 37℃.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total mRNA was extracted using TRIZOL Reagent (Cat#15596-018) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies). Illumina Hiseq 4000 SBS Kit (Cat#FC-410-1003) was used 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 NovaSeq 6000 |
| |
|
| Data processing |
Illumina platform used for base-calling, fastx_toolkit_0.0.14, SeqPrep, and Sickle softwares used for quality control of sequence reads.
Clean data was assambled for mapped data with Hisat2 software, then mapped to GRCh38.p10 whole genome using Cufflinks software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with RSEM software. Exons from all isoforms of a gene were merged to create one meta-transcript considering paired-end reads, reads length, and fragment length.
Genes were considered significantly differentially expressed under the following criteria: p-adjust < 0.05 & |log2FC| >= 1.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: xls file includes TPM values for each Sample.
|
| |
|
| Submission date |
Mar 10, 2021 |
| Last update date |
Jun 12, 2024 |
| Contact name |
yang tang |
| E-mail(s) |
tangyang2013@sibcb.ac.cn
|
| Organization name |
Shanghai Institute of Biochemistry and Cell Biology
|
| Street address |
Yueyang Road 320
|
| City |
shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE168618 |
Whole transcriptomes analyses of HGC-27 cell line treated with control DMSO, disulfiram, thiram or CX-6258 |
|
| Relations |
| BioSample |
SAMN18239652 |
| SRA |
SRX10303542 |
