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Sample GSM2233240 Query DataSets for GSM2233240
Status Public on Jul 12, 2017
Title primary_RHH1527
Sample type SRA
 
Source name squamous cell carcinoma, primary tumor
Organism Homo sapiens
Characteristics disease status: squamous cell carcinoma
tissue: primary tumor
sample type: single cell
Extracted molecule total RNA
Extraction protocol RNA isolated from cells using the SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (Clontech).
Library construction: In accordance to protocol from Fluidigm describing the use of the C1 system to generate cDNA library for single cell RNA-seq. Briefly, cDNA was synthesized using SMARTer Ultra Low RNA Kit for the Fluidigm C1 System from Clontech; library was constructed using Nextera XT DNA Sample Preparation Kit and Nextera XT DNA Library Preparation Index Kits from Illumina.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description Primary cancer
PolyA+ RNA
Processed data file: expression.txt
Data processing BAM files produced using Tophat-2.1.0.
FPKM obtained using Cuffdiff-2.2.1.
The RefSeq genes are tracked for analysis.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: expression.txt: The tab-delimited text file contains the log2(1+pQ normalized FPKM) expression matrix for all individual cells. For details about pQ normalization, see Sengupta, Debarka, et al. "Fast, scalable and accurate differential expression analysis for single cells." bioRxiv (2016): 049734.
 
Submission date Jul 14, 2016
Last update date May 15, 2019
Contact name Debarka Sengupta
E-mail(s) debarka@gmail.com
Organization name Indraprastha Institute of Information Technology
Department Computational Biology and Computer Science
Street address IIIT Delhi, Okhla Phase 3
City Delhi
State/province Delhi
ZIP/Postal code 110020
Country India
 
Platform ID GPL20301
Series (1)
GSE84323 Phenotype-driven precision oncology in patient-derived tumor models predict therapeutic response in squamous cell carcinoma
Relations
BioSample SAMN05391974
SRA SRX1949017

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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