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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 29, 2019 |
| Title |
patient3_tumor |
| Sample type |
SRA |
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| Source name |
gallbladder tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: gallbladder
disease state: tumor
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the tissue using the Qiagen RNA purificaction kit.
Libraries for RNA-Seq were prepared with Kapa hyper Prep Kits with RiboErase. The workflow consists of rRNA depletion, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
FPKM_normalized_expression.txt
s1A
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| Data processing |
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 UCSC trasncripts set using bowtie2. RSEM was uesd to estimated the gene expression and DCC was ued to circRNA prediction and circRNA expression calculation.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Samples
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| Submission date |
Jun 22, 2017 |
| Last update date |
Oct 29, 2019 |
| Contact name |
Xiangming Ding |
| Organization name |
UCLA
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| Street address |
650 Charles E Young Dr S, Los Angeles, CA 90095
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| City |
Los angeles |
| State/province |
CA |
| ZIP/Postal code |
91436 |
| Country |
USA |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE100363 |
Identification of differentially expressed circRNA in gallbladder cancer compared with matched normal tissue |
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| Relations |
| BioSample |
SAMN07269612 |
| SRA |
SRX2947603 |
| 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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