|
| Status |
Public on May 18, 2015 |
| Title |
HeLa-Negative Control |
| Sample type |
SRA |
| |
|
| Source name |
HeLa-Negative Control
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa cervical cancer cell line
transfection: miR-603 negative control
|
| Treatment protocol |
Cells are transfected with miR-603 negative control or miR-603 mimic for 48 hours.
|
| Growth protocol |
Cells are growing for 24 hours and then are used for transfection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each sample using TRIzol Reagent (Life technologies, USA) according to the proto- col from manufacturer. The concentration of each sample was measured by NanoDrop 2000 (Thermo Scientific, USA). The quality was assessed by the Agilent2200 (Agilent, USA).
The cDNA library was prepared using the Ion Total RNA-Seq Kit v2 (Lifetech, Carlsbad, CA, USA, Cat. No. 4479789) following the manufacturer’s instructions
Instrument model: ABI IonProton.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
The raw reads ≥50 bp which passed filtering were used for mapping. We used the Masplicing as our RNA-seq data mapping analysis tool whose core program is Bowtie that can identify the exon-exon splicing immediately and accurately
We applied the EBseq to filter the differentially expressed genes for the case and control groups. After the statistical analysis, we selected the differentially expressed genes according to the FDR threshold (FDR < 0.05)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and count number for each Sample.
|
| |
|
| Submission date |
May 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
jin fan |
| E-mail(s) |
houpw89@163.com
|
| Organization name |
novelbio informatics company
|
| Street address |
dongchuan Road
|
| City |
shanghai |
| ZIP/Postal code |
200000 |
| Country |
China |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE68987 |
RNA sequencing analysis of miR-603 overexpression |
|
| Relations |
| BioSample |
SAMN03700704 |
| SRA |
SRX1032422 |
