|Public on Sep 19, 2018
|SCARNA13 ASO rep 3
|cell line: HCCLM3 cells
transfection: SCARNA13 ASO
|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
|Illumina NovaSeq 6000
|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.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|Sep 18, 2018
|Last update date
|Mar 15, 2019
|West China Hospital
|Department of Liver Surgery & Liver Transplantation
|Laboratory of Liver Surgery
|No. 37 of Guoxue Lane
|Gene expression profiling of HCCLM3 cells: Control ASO vs SCARNA13 ASO
|Gene expression profiling of xenografts generated by lung metastasis screening models and HCCLM3 cells