|
| Status |
Public on Jul 01, 2018 |
| Title |
NMR_KYSE450 |
| Sample type |
SRA |
| |
|
| Source name |
esophageal squamous cell carcinoma cells_NMR_overexpression_KYSE450
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KYSE450
cell type: esophageal squamous cell carcinoma cells
tissue: esophagus
passages: 5-10
|
| Treatment protocol |
For knockdown of NMR, the recombined plasmid and the packing plasmid mixture (Invitrogen) were co-transfected into HEK 293T cells using Lipofectamine 3000 (Invitrogen). The supernatant containing lentivirus was collected and used to infect ESCC cell lines; For overexpression of NMR, plasmid vectors PCDNA3.1 were transfected into ESCC cancer cells using Lipofectamine 3000 (Invitrogen) according to the manufacturer’s instructions.
|
| Growth protocol |
Human ESCC cell lines KYSE70 and KYSE450 were cultured at 37 ℃ in an atmosphere of 5% CO2 in RMPI 1640 (Hyclone) supplemented with 10% FBS (Gibco), penicillin, and streptomycin (Thermo Fisher).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each sample was extracted with Trizol (Thermo Fisher), quality control for total RNA was assessed using NanoPhotometer® spectrophotometer, Qubit® 2.0 Fluorometer, and Agilent 2100 bioanalyzer. RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human genome (hg19) using TopHat v2.0.9.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene.And then Reads Per Kilobase of exon model per Million mapped reads,(RPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
|
| |
|
| Submission date |
Jul 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuan Li |
| Organization name |
National cancer center/cancer hospital
|
| Street address |
Panjiayuannanli No.17
|
| City |
Beijing |
| ZIP/Postal code |
100021 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE101743 |
LncRNA NMR knockdown and overexpression in esophageal squamous cell carcinoma cell lines |
|
| Relations |
| BioSample |
SAMN07375358 |
| SRA |
SRX3026756 |
