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| Status |
Public on May 22, 2015 |
| Title |
SEQC_NB024 |
| Sample type |
SRA |
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| Source name |
neuroblastoma
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| Organism |
Homo sapiens |
| Characteristics |
tissue: neuroblastoma
dataset: 2
Sex: F
age at diagnosis: 499
mycn status: 0
high risk: 0
inss stage: 1
class label: N/A
progression: 0
death from disease: 0
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| 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.
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| Growth protocol |
N/A
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Aug 09, 2013 |
| Last update date |
May 22, 2015 |
| Contact name |
Leming Shi |
| E-mail(s) |
lemingshi@fudan.edu.cn
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| Phone |
+86-18616827008
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| Organization name |
Fudan University
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| Department |
School of Life Sciences
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| Lab |
Center for Pharmacogenomics
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| Street address |
2005 Songhu Road
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| City |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
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| 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] |
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| Relations |
| BioSample |
SAMN02315029 |
| Supplementary data files not provided |
| Raw data not provided for this record |
| Processed data are available on Series record |
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