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Sample GSM1963870 Query DataSets for GSM1963870
Status Public on Dec 09, 2016
Title BC03LN_28
Sample type SRA
 
Source name BC03LN_Single-cell RNA-seq
Organism Homo sapiens
Characteristics patient id: BC03LN
molecular subtype: double positive (ER+ and HER2+)
cell type: metastatic breast cancer
Growth protocol On the day of surgery, all single cells were dissociated with mechanical and enzymatical method then immediately used for assay without any in vitro culture.
Extracted molecule total RNA
Extraction protocol Dead cells in single cell suspensions were removed by Ficoll-Paque TM PLUS (GE healthcare) separation before loading to integrated fluidic circuit (IFC) chip. Each suspension was loaded to 10-17um IFC for mRNA sequencing chip then cDNA synthesis and amplification were performed with SMARTer Ultra Low RNA Kit (Clontech) in the C1TM Single-Cell Auto Prep System (Fluidigm). RNA spike-ins 1, 4 and 7 from ArrayControl TM RNA Spikes (ThermoFisher) were added to the lysis mix for validation of array and batch effect. Bulk RNAs were extracted from ~1x10^5 cells of suspensions or tumor tissues using RNeasy Plus Micro kit (Qiagen) and 10ng of total RNAs were amplified with SMARTer kit (Clonetech) under the same conditions as single cells. All of amplified cDNAs were quantified and qualified by the Qubit® 2.0 Fluorometer (Life Technologies) and 2100 Bioanalyzer (Agilent Technologies). Total 549 single cell cDNAs and 14 bulk samples were subjected to the RNA sequencing.
Starting with 0.375 ng of amplified cDNAs, sequencing libraries were constructed with the Nextera XT DNA Sample Prep Kit (Illumina). All of constructed libraries were quantified and qualified by the Qubit® 2.0 Fluorometer (Life Technologies) and 2100 Bioanalyzer (Agilent Technologies) then pooled without index overlapping. Finally pooled libraries were sequenced using the HiSeq2500 (Illumina) as 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Single-cell RNA-seq
Data processing A modified reference was generated by merging the three array control RNA spike-ins (ThermoFisher) and the human genome reference (hg19) with the GENCODE 19 annotations.
Paired-end 100bp reads were aligned to the modified reference by 2-pass mode of STAR_2.4.0b with default parameters.
Transcripts Per Million (TPM) values were estimated using RSEM v1.2.17 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: A processed file is tab-delimited and contains the raw TPM values for 549 single cells and 14 bulk tumors.
 
Submission date Dec 03, 2015
Last update date May 15, 2019
Contact name Woosung Chung
Organization name Samsung Genome Institute
Street address Samsung Medical Center
City Seoul
State/province State...
ZIP/Postal code ASI|KR|KS013|SE
Country South Korea
 
Platform ID GPL16791
Series (1)
GSE75688 Single cell RNA sequencing of primary breast cancer.
Relations
BioSample SAMN04316772
SRA SRX1462744

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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