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Sample GSM1689729 Query DataSets for GSM1689729
Status Public on May 18, 2015
Title HEK293-Negative Control
Sample type SRA
 
Source name HEK293-Negative Control
Organism Homo sapiens
Characteristics cell line: HEK293 embryonic kidney 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 SAMN03700702
SRA SRX1032420

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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