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| Status |
Public on Sep 06, 2012 |
| Title |
LC_S47_nor |
| Sample type |
SRA |
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| Source name |
Adjacent lung normal cells
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| Organism |
Homo sapiens |
| Characteristics |
age_at_diagnosis: 75
gender: female
smoking_status: never smoker
Stage: NA
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNAs were extracted from tissue using RNAiso Plus (Takara Bio Inc.), followed by purification using RNeasy MinElute (Qiagen Inc.). RNAs were assessed for quality and was quantified using an RNA 6000 Nano LabChip on a 2100 Bioanalyzer (Agilent Inc.).
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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 |
Illumina Casava1.8 software used for basecalling.
RNA sequencing reads were aligned to the NCBI human reference genome assembly (build 37.1) using GSNAP (Wu and Nacu, Bioinformatics, 2010) with allowance for 5% mismatches.
RNA sequencing reads were also aligned to a cDNA set consisting of 161,250 mRNA sequences obtained from public databases (36,742 RefSeq, 73,671 UCSC, and 161,214 Ensembl) to decrease the false positives and false negatives in variant detection from RNA sequencing data (Ju et al., Nature Genetics, 2011; Ju et al., Genome Researcg, 2012).
For each gene, the number of reads aligned to it (raw read count) was normalized by RPKM (reads per kilobase per million mapped reads) (Mortazavi et al., Nature Methods, 2008).
Genome_build: human NCBI genome build 37.1
Supplementary_files_format_and_content: The 'LC-87_RPKM_expression.txt' file includes RPKM values for each sample. "accession" represents NCBI RefSeq accession number, "chrom" represents chromosome number, "start" represents the gene's genomic start position, "end" represents the gene's genomic end position and "strand" represents the gene's trascribed strand.
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| Submission date |
Aug 28, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Won-Chul Lee |
| E-mail(s) |
wclee47@gmail.com
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| Organization name |
MD Anderson Cancer Center
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| Street address |
1881 East Road
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| City |
Houston |
| ZIP/Postal code |
77054 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE40419 |
The transcriptional landscape and mutational profile of lung adenocarcinoma |
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| Relations |
| SRA |
ERX140421 |
| BioSample |
SAMN02197274 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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