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Sample GSM1887345 Query DataSets for GSM1887345
Status Public on Sep 18, 2015
Title Pt_mRCC_SC_84
Sample type SRA
 
Source name patient, metastatic RCC_29
Organism Homo sapiens
Characteristics cell type: metastatic renal cell carcinoma
cell source: patient
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.
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). 
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description scRNA-seq
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.
 
Submission date Sep 17, 2015
Last update date May 15, 2019
Contact name Kyu-Tae Kim
Organization name Samsung Medical Center
Department Samsung Genome Institute
Street address Irwon-Ro 81
City Seoul
ZIP/Postal code 135-710
Country South Korea
 
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
Relations
BioSample SAMN04093600
SRA SRX1253781

Supplementary file Size Download File type/resource
GSM1887345_Pt_mRCC_SC_84.TPM.txt.gz 1.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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