|
| Status |
Public on Jun 01, 2015 |
| Title |
saiGP-RZ RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 cells total RNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HEK293
transfection time: 48 hours
plasmids used: pH1-saiGP-RZ
transfection dosage: 400 ng plasmids per well in 6-well cell culture plate
|
| Treatment protocol |
HEK293 cells in 6-well plate were transiently transfected with 400 ng plasmids of control, shRNA, shRNA-LC, saiRNA-RZ for 48 hr.
|
| Growth protocol |
HEK293 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM, GIBCO) supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit (NEB) according to the manufacturer’s protocol.
HEK293 cells were washed once with PBS and then treated with Trizol reagent for total RNA extracting.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq raw fastq reads were uniquely mapped to hg19 whole human genome using Tophat with up to 2 nt mismatches and assembled into transcripts using cufflinks with known transcriptome annotation. Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated for each known genes.
For RNA-seq, tab-delimited text files include FPKM values of known genes, and gene_name represents known gene name, FPKM represents gene expression.
Illumina Casava1.7 software used for basecalling.
Genome_build: hg19
|
| |
|
| Submission date |
May 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Fengjuan Zhang |
| Organization name |
Shanghai Institutes for Biological Sciences, CAS
|
| Department |
Institute of Biochemistry and Cell Biology
|
| Lab |
Ligang Wu
|
| Street address |
320 Yueyang Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE68631 |
Ribozyme-enhanced single-stranded Ago2-processed interfering RNA triggers efficient gene silencing with fewer off-target effects. |
|
| Relations |
| BioSample |
SAMN03610667 |
| SRA |
SRX1020618 |
