|
| Status |
Public on Oct 30, 2018 |
| Title |
5Y_pancEts-1 |
| Sample type |
SRA |
| |
|
| Source name |
SH-SY5Y stably transfected with pancEts-1
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: neuroblastoma
cell line: SH-SY5Y
passages: 15-18
|
| Treatment protocol |
The pancEts-1 expression or empty vectors were transfected into tumor cells, and stable cell lines were screened by administration of neomycin.
|
| Growth protocol |
Human neuroblastoma cell line SH-SY5Y was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
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 |
| |
|
| Description |
Gene expression after stable transfection of pancEts-1
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Oct 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Qiangsong Tong |
| E-mail(s) |
qs_tong@hotmail.com
|
| Organization name |
Union Hospital of Tongji Medical College
|
| Department |
Department of Surgery
|
| Street address |
1277 Jiefang Avenue
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430022 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE104950 |
Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of Ets-1 promoter-associated noncoding RNA (pancEts-1) |
|
| Relations |
| BioSample |
SAMN07782187 |
| SRA |
SRX3280928 |
