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| Status |
Public on Sep 18, 2015 |
| Title |
PDX_pRCC_SC_55 |
| Sample type |
SRA |
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| Source name |
PDX, primary RCC_23
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| Organism |
Homo sapiens |
| Characteristics |
cell type: primary renal cell carcinoma
cell source: patient-derived xenograft
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| Growth protocol |
This study was carried out in accordance with the principles of the Declaration of Helsinki, and approved by The Samsung Medical Center (Seoul, Korea) Institutional Review Board (IRB) (no. 2010-04-004). A participant in this study gave written informed consent for research and publication of the results. Animal experiments were conducted in accordance with the Institute for Laboratory Animal Research Guide for the Care and Use of Laboratory Animals and within the protocols approved by the appropriate IRB at the Samsung Medical Center. After validating the origin of each xenograft by short tandem repeat DNA fingerprinting, sacrified tumor tissues together with prepared patient metastasis tumor samples were dissociated to implement C1™ Single-Cell Auto Prep System.
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| Extracted molecule |
total RNA |
| Extraction protocol |
In order to isolate single-cells and amplify initial RNA content enough to transcriptome sequencing, we adopted the C1TM Single-Cell Auto Prep System (Fluidigm, CA, USA) with the SMARTer kit (Clontech, CA, USA). Cells were captured on the C1 chip (17-25 μm) and determined as a live single cell by fluorescence microscopic observation. Quantity and quality of amplified cDNAs from individual single cells were checked by Qubit® 2.0 Fluorometer (Life Technologies, CA, USA) and 2100 Bioanalyzer (Agilent Inc., CA, USA). RNAs from bulk cell samples were also amplified using a SMARTer kit with 10 ng of starting material. For WES, gDNAs were prepared using QIAamp® DNA Mini kit (QIAGEN, CA, USA). Exome sequencing was carried using the SureSelect XT Human All Exon V5 kit (Agilent Inc., CA, USA), according to the manufacturer’s standard protocol.
Libraries were prepared using the Nextera XT DNA Sample Prep Kit (Illumina, CA, USA) following the manufacturer’s instruction, assayed the quantity and quality, pooled, and then sequenced on the HiSeq 2500 (Illumina) using the 100bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina) at the Samsung Genome Institute (Seoul, Korea). Sequencing of the exome library was carried out on the HiSeq 2500 (Illumina, CA, USA) using the 100bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina) at the Samsung Genome Institute (Seoul, Korea).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
scRNA-seq
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| Data processing |
For PDX samples, RNA-seq reads only mapped to the mouse genome reference (mm10) were removed. Then, sequencing reads were aligned to the human genome reference (hg19) together with splice junction information of each sample using the 2-pass mode of STAR_2.4.0d (Dobin et al., Bioinformatics 2012). Transcripts Per Million (TPM) was quantified by implementing RSEM v1.2.18 (Li et al., BMC Bioinformatics 2011) in default mode with Genecode v.19 annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Each row of the tab-delimited text file includes ENSEMBL gene ID,ENSEMBL transcript ID, transcript length, effective_length, expected_count, TPM, FPKM for samples.
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| Submission date |
Sep 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kyu-Tae Kim |
| Organization name |
Samsung Medical Center
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| Department |
Samsung Genome Institute
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| Street address |
Irwon-Ro 81
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| City |
Seoul |
| ZIP/Postal code |
135-710 |
| Country |
South Korea |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE73121 |
Single-cell transcriptome profiling for metastatic renal cell carcinoma patient-derived cells [RNA-seq] |
| GSE73122 |
Single-cell transcriptome profiling for metastatic renal cell carcinoma patient-derived cells |
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| Relations |
| BioSample |
SAMN04093666 |
| SRA |
SRX1253727 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1887274_PDX_pRCC_SC_55.TPM.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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