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Sample GSM3391778 Query DataSets for GSM3391778
Status Public on Sep 19, 2018
Title Xeno-Hep3B rep 2
Sample type SRA
Source name Hep3B cells
Organism Homo sapiens
Characteristics cell type: Hep3B 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
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
BioSample SAMN10081237
SRA SRX4707260

Supplementary file Size Download File type/resource
GSM3391778_Xeno-Hep3B_rep_2.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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