|
| Status |
Public on Jan 30, 2016 |
| Title |
HCC-C2-R-14P-2 |
| Sample type |
SRA |
| |
|
| Source name |
HCC-C2 Non-recurrent Tumor's Adjacent Normal
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: HCC Non-recurrent Tumor's Adjacent Normal
individual: HCC-C2
gender: M
age: 55
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: I-II
primary tumor cirrhosis: Yes
recurrent tumor method: 0
recurrent tumor organ: 0
recurrent tumor size (cm): 0
recurrent tumor content (%): 0
recurrent tumor grade: 0
recurrent tumor cirrhosis: 0
glu: 4.55
alt: 78
ast: 134
ggt: 64.2
tb: 35.8
db: 14.1
alb: 22.3
hgb: 113
pt: 17
hbsag: >240
hbvdna: 1040000
afp: 5.2
cea: 4.79
ca199: 72.6
bclc stage pre-ltx: D
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 |
SAMN02720931 |
| SRA |
SRX512246 |
