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| Status |
Public on Dec 06, 2023 |
| Title |
Responder, A19_121T |
| Sample type |
SRA |
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| Source name |
tumor
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| Organism |
Homo sapiens |
| Characteristics |
tissue: tumor
disease state: HCC
group: Responder
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| Extracted molecule |
total RNA |
| Extraction protocol |
Flash frozen on dry ice, and RNA was harvested using Trizol reagent.
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 2000 |
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| Data processing |
Original data file from Illumina is transformed into sequenced reads (raw data, FASTQ formate files) by CASAVA base recognition.
Raw data is filtered by removal of reads with adaptor contamination,reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%),reads when low quality nucleotides (Base Quality less than 20) constitute more than 50 percent of the read. The Qscore (Quality value) of over 50% bases of these read is <= 5.
Sequencing is mapped to Homo_sapiens_hg19 by STAR software. The alignment by STAR performs precise and effective in positioning junction reads for RNA sequencing data analysis.
FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments (Mortazavi et al. 2008).
For the samples with biological replicates, differential expression analysis of two conditions/groups was performed using the Limma R package.
Assembly: Homo_sapiens_hg19
Supplementary files format and content: A txt file of gene expression level (FPKM value) of all samples.
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| Submission date |
Oct 07, 2022 |
| Last update date |
Dec 06, 2023 |
| Contact name |
Chunxiao Liu |
| E-mail(s) |
liuchunxiao_1989@126.com
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| Phone |
5713763441
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| Organization name |
MD Anderson Cancer center
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| Street address |
6565 MD Anderson Blvd., Zayed building. Z11.4000A
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| City |
HOUSTON |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE215011 |
Next Generation Sequencing Facilitates Quantitative Analysis of tumor samples from HCC patients receiving Nivolumab. |
| GSE215013 |
Tumor samples from HCC patients receiving Nivolumab; THP-1 cells under different stimulas. |
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| Relations |
| BioSample |
SAMN31207406 |
| SRA |
SRX17826741 |
| 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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