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Sample GSM1206089 Query DataSets for GSM1206089
Status Public on May 22, 2015
Title SEQC_NB354
Sample type SRA
 
Source name neuroblastoma
Organism Homo sapiens
Characteristics tissue: neuroblastoma
dataset: 2
Sex: F
age at diagnosis: 267
mycn status: 0
high risk: 0
inss stage: 4
class label: 1
progression: 1
death from disease: 1
Treatment protocol All neuroblastoma samples of this set were obtained prior to any cytotoxic treatment and were snap-frozen immediately after surgery. Prior to RNA extraction tumor cell content was checked by a pathologist and only samples with >60% tumor content were processed further.
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol 30-60mg of snap-frozen neuroblastoma specimen was cryo-sectioned and were homogenized in TRIzol reagent (Invitrogen, Karlsruhe, Germany) using the FastPrep FP120 cell disruptor (Qbiogene, Inc, Carlsbad, CA, USA).Total RNA was isolated following the TRIzol protocol (Invitrogen) and RNA integrity was assessed using the 2100 Bioanalyzer (Agilent, Waldbronn, Germany). Only samples with an RNA Integrity Number >7.5 were taken for further analysis.
Library construction was performed according to the standard TruSeqTM protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Software used for basecalling are HCS1.4.8+RTA1.12.4.2, HCS1.4.8+RTA1.12.4.2 and HCS1.5+RTA1.13.48.
Sequenced reads were masked for low-complexity or low-quality sequence (entropy < 15), then mapped to the genome, the RefSeq and AceView 2011 gene models, the mitochondrial genes, the rRNA and RNA genes, the spike-in sequence, and finally the imaginary genome as a mapping specificity control. For each read repair, alignment on all targets, genes or genome, are scored, and only the best scores are kept.
The Magic expression index for the gene is measured as the log base 2 of the number of bases aligned in the gene, divided by the number of terabases aligned in known genes and by the length of the gene, with several corrections. Genes that are not significantly expressed, i.e., with less than 4 reads above the experimental noise level, acquire an N/A flag.
Genome_build: human genome (NCBI 37)
Supplementary_files_format_and_content: tab-delimited text files include index values for each sample
 
Submission date Aug 09, 2013
Last update date May 22, 2015
Contact name Leming Shi
E-mail(s) lemingshi@fudan.edu.cn
Phone +86-18616827008
Organization name Fudan University
Department School of Life Sciences
Lab Center for Pharmacogenomics
Street address 2005 Songhu Road
City Shanghai
ZIP/Postal code 200438
Country China
 
Platform ID GPL17553
Series (2)
GSE47792 SEQC Project
GSE49711 RNA-Seq reveals an unprecedented complexity of the neuroblastoma transcriptome and is suitable for clinical endpoint prediction [RNA-Seq]
Relations
BioSample SAMN02314622

Supplementary data files not provided
Raw data not provided for this record
Processed data are available on Series record

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