|
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 |