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Sample GSM1328793 Query DataSets for GSM1328793
Status Public on Aug 15, 2014
Title 078222N
Sample type SRA
 
Source name liver tissue
Organism Homo sapiens
Characteristics tissue: paratumoral liver tissue
Treatment protocol tumor and paratumoral tissue were resected and RNAlater reagents treated immediately for overnight, followed by -80 freezer storage before use
Extracted molecule polyA RNA
Extraction protocol trizal reagent to prepare total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to hg19 whole genome using Tophat v2.0.4 with parameters -i 10 -I 80000 --solexa1.3-quals --min-coverage-intron 20 --max-coverage-intron 11000 --min-segment-intron 10 --max-segment-intron 81000 --segment-length 20 -G genes.gtf -g 10 -p 15
Gene annotation and calculation of FPKM values was carried out using Cufflinks (v2.0.2) with the provision of a GTF annotation file (hg19).
Gene expression differences were assessed by Cuffdiff, with false discovery rate correction for multiple testing.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
 
Submission date Feb 14, 2014
Last update date May 15, 2019
Contact name Tao Cai
E-mail(s) caitao@nibs.ac.cn
Organization name National Institute Of Biological Sciences, Beijing (NIBS)
Lab Sequencing Facility
Street address No. 7 Science Park Road, Zhongguancun Life Science Park
City Beijing
ZIP/Postal code 102206
Country China
 
Platform ID GPL9115
Series (1)
GSE55048 Transcriptomic characterization of Hepatocellular Carcinoma with CTNNB1 mutation
Relations
BioSample SAMN02642750
SRA SRX471344

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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