|
| Status |
Public on Jun 30, 2015 |
| Title |
CNE1-MOCK |
| Sample type |
SRA |
| |
|
| Source name |
CNE1-MOCK_RNA-seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CNE1
cell type: human nasopharyngeal carcinoma cells
passages: 3
infected with: control lentivirus
|
| Treatment protocol |
CNE1 cells were infected with EBV-miR-BART1/3/7 and their control lentivirus seperately according to the manufacture's protocol.
|
| Growth protocol |
Human nasopharyngeal carcinoma cell line CNE1 was cultured in RPMI 1640 with 10% new born cow serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolated with TRIzol reagent was treated with RNase-free DNase (NEB) at 37 oC for 10 minutes. The Dynabeads mRNA Purification Kit (Life Technologies) was used to isolate mRNA from the total RNA samples.
According to the manufacturer’s instructions, the mRNA was chemically fragmented by the use of divalent cations and converted into single-stranded cDNA using random hexamer primers and SuperscriptⅡ reverse transcriptase (Life Technologies). The second strand was generated to create double-stranded cDNA using RNase H (Enzymatics) and DNA polymerase. The cDNA products was purified by Ampure beads XP (Beckman).After converting the overhangs into blunt ends using T4 DNA polymerase and Klenow DNA polymerase, an ‘A’ base was added to the 3’ end of the DNA fragments by the polymerase activity of Klenow fragment. Sequencing adapters were subsequently ligated to the ends of the cDNA fragments using T4 DNA Ligase (Enzymatics). The fragments of 200bp were selected by Ampure beads XP (Beckman) and enriched by 12 cycles of PCR. The PCR products were loaded into flowcell to generate clusters and then sequenced by Hiseq 2000 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 1
|
| Data processing |
The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
To get the clean reads, removing the dirty raw reads is needed before data analysis. Filter steps: 1. Remove reads with adaptors; 2. Remove reads in which unknown bases are more than 10%; 3. Remove low quality reads (the percentage of the low quality bases of quality value <5 is more than 50% in a read)
Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM values for each Sample .
|
| |
|
| Submission date |
Dec 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Xin Li |
| E-mail(s) |
xinli268@gmail.com
|
| Phone |
86 20 62789438
|
| Organization name |
Southern medical university
|
| Department |
Cancer research institute
|
| Street address |
Southern medical university
|
| City |
Guangzhou |
| State/province |
Province |
| ZIP/Postal code |
510515 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE42945 |
The novel functional effects of exogenous EBV-miR-BARTs on NPC progression |
| GSE43126 |
Next Generation Sequencing Facilitates Quantitative Analysis of CNE1-mock, CNE1-BART1, CNE-BART3, CNE1-BART7 cells |
|
| Relations |
| SRA |
SRX212471 |
| BioSample |
SAMN01853566 |
