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Status |
Public on Jan 30, 2016 |
Title |
HCC4-R-13T-4 |
Sample type |
SRA |
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Source name |
HCC4 Recurrent Tumor
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Organism |
Homo sapiens |
Characteristics |
tissue: HCC Recurrent Tumor individual: HCC4 gender: M age: 59 hbv (pre-olt): Positive hbv (post-olt): Positive primary tumor and nat rna: Yes primary tumor biopsy method: OLT primary tumor content (%): 90 primary tumor size (cm): 8 primary tumor grade: II primary tumor cirrhosis: No recurrent tumor method: RFA recurrent tumor organ: liver recurrent tumor size (cm): 2.5 recurrent tumor content (%): NA recurrent tumor grade: NA recurrent tumor cirrhosis: No glu: 5.4 alt: 20 ast: 19 ggt: 37.7 tb: 17.4 db: 3.9 alb: 43.7 hgb: 145 pt: 11.6 hbsag: 15.22(+) hbvdna: <500 afp: 2.5 cea: 1.27 ca199: 8.4 bclc stage pre-ltx: B definitions: RFA=Radiofrequency ablation; VATS=Video-assisted thorascopic surgery; OLT=Orthotopic liver transplantation; AFP=Alpha-fetoprotein
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 1000 |
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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
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Submission date |
Apr 07, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Dong Shen |
E-mail(s) |
shend@medimmune.com
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Phone |
301-398-1269
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Organization name |
Medimmune
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Department |
Translational Science
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Lab |
Pharmacogenomics
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Street address |
MedImmune Way
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City |
Gaithersburg |
State/province |
MD |
ZIP/Postal code |
21878 |
Country |
USA |
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Platform ID |
GPL15433 |
Series (1) |
GSE56545 |
mRNA profiling of Hepatocellular carcinoma (HCC) |
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Relations |
BioSample |
SAMN02720917 |
SRA |
SRX512221 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available on Series record |
Processed data provided as supplementary file |
Raw data are available in SRA |
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