|
| Status |
Public on Mar 20, 2020 |
| Title |
ISLR_3 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293FT cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: embryonal kidney cells
agent: ISLR
cell line: HEK293FT
|
| Treatment protocol |
Cells were treat with ISLR secreted supernatant or empty vector control supernatant for 72 hours
|
| Growth protocol |
Cells were incubated with DMEM 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 |
Aug 02, 2019 |
| Last update date |
Mar 20, 2020 |
| Contact name |
yang tang |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE135280 |
Whole transcriptomes analyses of HEK293FT cell line treated with ISLR secreted supernatant or empty vector control supernatant |
|
| Relations |
| BioSample |
SAMN12430174 |
| SRA |
SRX6640406 |
