|
Status |
Public on Jan 30, 2016 |
Title |
HCC1-R-13P-1 |
Sample type |
SRA |
|
|
Source name |
HCC1 Recurrent Tumor's Adjacent Normal
|
Organism |
Homo sapiens |
Characteristics |
tissue: HCC Recurrent Tumor's Adjacent Normal individual: HCC1 gender: M age: 48 hbv (pre-olt): Positive hbv (post-olt): Negative primary tumor and nat rna: Yes primary tumor biopsy method: OLT primary tumor content (%): 90 primary tumor size (cm): 5 primary tumor grade: III primary tumor cirrhosis: Yes recurrent tumor method: RFA recurrent tumor organ: liver recurrent tumor size (cm): 2 recurrent tumor content (%): NA recurrent tumor grade: NA recurrent tumor cirrhosis: No glu: 5.19 alt: 37 ast: 39 ggt: 133 tb: 22.8 db: 5.7 alb: 40.6 hgb: 131 pt: 12.1 hbsag: >240(+) hbvdna: <1000 afp: 2935.9 cea: 2.07 ca199: 33.2 bclc stage pre-ltx: A3 definitions: RFA=Radiofrequency ablation; VATS=Video-assisted thorascopic surgery; OLT=Orthotopic liver transplantation; AFP=Alpha-fetoprotein
|
Extracted molecule |
total RNA |
Extraction protocol |
Tumor and normal samples were removed, flash frozen on dry ice, and RNA was harvested. 1 ug of total RNA for the construction 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 HiSeq 1000 |
|
|
Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Human genome reference hg19 via Bowtie Genome_build: hg19 Supplementary_files_format_and_content: The normalized readcount for each gene for each sample processed via Deseq
|
|
|
Submission date |
Apr 07, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Dong Shen |
E-mail(s) |
shend@medimmune.com
|
Phone |
301-398-1269
|
Organization name |
Medimmune
|
Department |
Translational Science
|
Lab |
Pharmacogenomics
|
Street address |
MedImmune Way
|
City |
Gaithersburg |
State/province |
MD |
ZIP/Postal code |
21878 |
Country |
USA |
|
|
Platform ID |
GPL15433 |
Series (1) |
GSE56545 |
mRNA profiling of Hepatocellular carcinoma (HCC) |
|
Relations |
BioSample |
SAMN02720903 |
SRA |
SRX512212 |