|
| Status |
Public on Jun 12, 2017 |
| Title |
SHEE |
| Sample type |
SRA |
| |
|
| Source name |
SHEE cell lines
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SHEE
|
| Growth protocol |
SHEE and SHEEC were cultured in MEM medium (Gibco) supplemented with 100 ml/L fetal bovine serum (100 u/ml penicillin, 100 u/ml streptomycin) and incubated at 37oc in humidified atmosphere of 50 ml/L CO2. Cells were harvested when they grew into a full monolayer and kept at -70 until use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each sample was extracted using TRK1001 (LC Sciences, Cat. TRK-1001, Total RNA Purification Kit) according to the manufacturer's procedure. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
The SHEEC line was established through SHEE induced by 12-Otetradeanoy-lphorbol-13-acetate (TPA).This two cell lines is the most appropriate model of ESCC tumorigenesis.
|
| Data processing |
All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). All programs were performed with default setting (unless otherwise specified).
The unique mapped reads (85-90% of total reads) were subsequently assembled into transcripts guided by reference annotation (Gencode v20 and Refseq gene models) with Cufflinks v2.0.2 (Trapnell et al., 2012). Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
For the analyses of lncRNAs, cufflinks was used to estimate the transcript level FPKM values with the Gencode v20 lincRNA annotation (Derrien et al., 2012), and human body map lincRNA annotations (Cabili et al., 2011).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Aug 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiachun Sun |
| Organization name |
Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology
|
| Street address |
24 Jinghua road, Jianxi district
|
| City |
Luoyang |
| State/province |
Henan |
| ZIP/Postal code |
471003 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE72273 |
Globally construct ceRNA regulation network based on comparison with SHEE and SHEEC cell lines (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN04007151 |
| SRA |
SRX1162070 |
