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Sample GSM3393162 Query DataSets for GSM3393162
Status Public on Sep 19, 2018
Title SCARNA13 ASO rep 3
Sample type SRA
Source name HCC cells
Organism Homo sapiens
Characteristics cell line: HCCLM3 cells
transfection: SCARNA13 ASO
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 18, 2018
Last update date Mar 15, 2019
Contact name Tian Lan
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)
GSE120095 Gene expression profiling of HCCLM3 cells: Control ASO vs SCARNA13 ASO
GSE120096 Gene expression profiling of xenografts generated by lung metastasis screening models and HCCLM3 cells
BioSample SAMN10081243
SRA SRX4707268

Supplementary file Size Download File type/resource
GSM3393162_SCARNA13_ASO_rep_3.txt.gz 2.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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