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| Status |
Public on Apr 24, 2022 |
| Title |
T15883 |
| Sample type |
SRA |
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| Source name |
lung tumor
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| Organism |
Homo sapiens |
| Characteristics |
batch: B
histology: Squamous Cell Carcinoma
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen lung tissues using TRIzol (Invitrogen) according to the manufacturer’s protocol. Only RNA samples with RNA sufficient RNA were included for analysis.
Libraries suitable for paired-ended sequencing were generated using Illumina’s TruSeq Stranded Total RNA Library Prep Kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
T15883_S27_lung_SC_U1_T1
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| Data processing |
The sequencing quality of each sample was assessed using FastQC.
Read- and alignment-level quality were assessed using FastQ Screen, Preseq, Picard tools, RSeQC and QualiMap.
Reads were trimmed for adapter sequences and low-quality bases using Cutadapt prior to alignment against the human reference genome, hg19, using STAR in two-pass mode with GENCODE v19 annotation
Gene expression levels were quantified using RSEM.
Assembly: Hg19
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| Submission date |
Apr 21, 2022 |
| Last update date |
Jun 10, 2022 |
| Contact name |
Josh Stone |
| E-mail(s) |
josh.stone@nih.gov, harrisc@nih.gov, khanm@mail.nih.gov
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| Phone |
240-760-7261
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| Organization name |
National Cancer Institue
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| Department |
CCR
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| Lab |
LHC
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| Street address |
9000 Rockville Pike
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE201221 |
Association of gene expression with Creatine Riboside, A Prognostic Metabolite of Metabolome Imbalance in the NCI-MD Non-Small Cell Lung Cancer Cohort |
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| Relations |
| BioSample |
SAMN27724637 |
| SRA |
SRX15657737 |
| 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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