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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 01, 2015 |
| Title |
K331NA |
| Sample type |
SRA |
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| Source name |
renal pelvis
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| Organism |
Homo sapiens |
| Characteristics |
tissue: renal pelvis
gender: M
age: 57
tnm: T3N0M0
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from UTUC and normal adjacent tissues using the TRIzol solution (Invitrogen, US) according to the manufacturer’s protocol, RNase-free DNase I was used to eliminate DNA contamination. The integrity RNA was evaluated using Agilent 2100 Bioanalyzer (Agilent Technologies, US).
RNA libraries were prepared for sequencing using standard Illumina protocols
Digital gene expression tag profiling
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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 |
Adaptor sequences were removed from the raw sequencing data, and potentially erroneous tags that have only single copy and those contain unknown sequences were filtered out.
Tags were mapped to the constructed reference after filtration using SOAP2 allowing no more than one mismatch
Normalized TPM (transcripts per million clean tags) values and fold change (absolute value of log2ratio, cancer versus normal) were calculated using uniquely mapping tags
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include TPM values for each Sample
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| Submission date |
Jun 06, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gaille Joo |
| E-mail(s) |
gaille.joo@gmail.com
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| Organization name |
BGI
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| Street address |
Beishan Industrial Zone, Yantian District
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| City |
Shenzhen |
| ZIP/Postal code |
518083 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE47702 |
ALDH2, CCNE1 and SMAD3 are Potential Prognostic Markers for Upper Tract Urothelial Carcinoma Revealed by Massively Parallel Sequencing. |
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| Relations |
| BioSample |
SAMN02191900 |
| SRA |
SRX297124 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1155158_K331NA.GeneExpression.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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