|
| Status |
Public on Jun 01, 2015 |
| Title |
saiLC-RZ small 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-saiLC-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 |
Small RNA libraries were prepared for sequencing using standard Illumina protocols.
HEK293 cells were washed once with PBS and then treated with Trizol reagent for total RNA extracting.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Small RNA-seq raw fastq reads were filtered low quality sequences, trimmed for adaptor sequence. Redundant sequences were collapsed as useful reads for further analysis. Reads that could not be clipped or with lengths shorter than 19 bp were removed. Useful reads were mapped into hg19 whole genome and shRNA or saiRNA sequences using Bowtie (version 0.12.7) without allowing any mismatches. The mapped genome reads were further categorized as miRNA, tRNA, rRNA and snoRNA as the written sequence.
For small RNA-seq, tab-delimited text files include read count of sequence, and read_sequence represents read sequence, read_count represents sequenced number of read.
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 |
SAMN03610674 |
| SRA |
SRX1020625 |
