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| Status |
Public on Oct 17, 2016 |
| Title |
L10-14-Tumor_RNA-seq |
| Sample type |
SRA |
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| Source name |
Biopsy of HCV+ HCC tumor
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| Organism |
Homo sapiens |
| Characteristics |
tissue: liver
disease state: Tumor
Sex: F
age: 55
hcv_viral_load: 1928995
staging: 2.5
interface_necrosis: 2
confluent_necrosis: 0
focal_lytic_nec_apop: 1
portal_inflammation: 2
total_grade: 5
hcv_genotype: 1
cea: NA
ca19_9: NA
afp: 21.8
sgot: 251
sgpt: 110
batch: 0
race: B
differentiation: 0
hcv_activity: 2
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| Extracted molecule |
total RNA |
| Extraction protocol |
We extracted total RNA from homogenized liver samples with 0.2 ml of chloroform and 1 ml of TRIZOL Reagent. After precipitation and washing, the RNA was dissolved in RNase-free water and given DNase treatment.
DNase-treated, rRNA-depleted (Ribozero, Epicentre) RNA was used as a template for SuperScript III first-strand cDNA synthesis (Invitrogen), using oligo-dT as well as random hexamers. Actinomycin D was added to the reaction to prevent any possible amplification from contaminating genomic DNA. During second-strand synthesis, a dU/VTP mix was used to create directional libraries. cDNA samples were fragmented with Covaris to 300-bp fragments. The samples were then end-filled, 3 terminal A extended and ligated to preannealed TruSeq-indexed Illumina adapters. Uracil-DNAglycosylase UDG) treatment preceded the PCR reaction to amplify exclusively the originally oriented transcripts. Libraries were amplified using P5 and P7 Illumina primers and gel-extracted for size selection and primer-dimer removal. Before sequencing, libraries were tested using the BioAnalyzer to assure library quality, in terms of size and primer-dimer depletion. Indexed libraries were multiplexed for 100-bp single-end sequencing on the Illumina HiSeq 2000 platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Before sequencing, libraries were tested using the BioAnalyzer to assure library quality, in terms of size and primer-dimer depletion and indexed libraries were multiplexed for 100 bp single-end sequencing on the Illumina HiSeq 2000 platform.
FASTQ files of past filter reads were obtained and aligned to a composite reference exome of human (hg19), mirBase and HCV using GSNAP.
Next, alignments were associated with genes using HTSeq.
We scaled gene counts using DESeq implemented in R to estimate effective library size.
Genome_build: hg19
Supplementary_files_format_and_content: Combined_processed_RNAseq_data.txt.gz: Matrix with columns corresponding to each sample and rows corresponding to each gene/
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| Submission date |
Jun 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Neil Ari Wijetunga |
| Organization name |
Albert Einstein College of Medicine
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| Department |
Genetics
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| Lab |
John Greally Price 214
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| Street address |
1301 Morris Park Ave
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| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE82177 |
Human liver RNA-seq data corresponding to uninfected non-malignant, HCV infected non-malignant, and HCV+ HCC tissue |
| GSE82178 |
Human liver RNA-seq and HELP-tagging data corresponding to uninfected non-malignant, HCV+ non-malignant, and HCV+ HCC tissue |
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| Relations |
| BioSample |
SAMN05199316 |
| SRA |
SRX1817191 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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