|
| Status |
Public on Sep 19, 2018 |
| Title |
Xeno-SK-Hep1 rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
SK-Hep1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: SK-Hep1 cells
screening: lung metastasis screening
|
| 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 Vonstruction 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 |
Illumina NovaSeq 6000 |
| |
|
| 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 Vontaining adapter, reads Vontaining 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.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Sep 17, 2018 |
| Last update date |
Sep 21, 2018 |
| Contact name |
Tian Lan |
| E-mail(s) |
blue_sky_land@163.com
|
| Organization name |
West China Hospital
|
| Department |
Department of Liver Surgery & Liver Transplantation
|
| Lab |
Laboratory of Liver Surgery
|
| Street address |
No. 37 of Guoxue Lane
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE120021 |
Gene expression profiling of xenografts generated by lung metastasis screening models |
| GSE120096 |
Gene expression profiling of xenografts generated by lung metastasis screening models and HCCLM3 cells |
|
| Relations |
| BioSample |
SAMN10081236 |
| SRA |
SRX4707261 |
