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| Status |
Public on Mar 01, 2018 |
| Title |
Patient 17 17N (RNA-seq) |
| Sample type |
SRA |
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| Source name |
adjacent normal
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| Organism |
Homo sapiens |
| Characteristics |
tissue: adjacent normal
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| Extracted molecule |
total RNA |
| Extraction protocol |
tumor samples and normal tissues were collected from the Oncology Department of the Second Affiliated Hospital of Zhen Zhou University by related surgeons. Plasma samples were isolated by EDTA and centrifuged at 820 ×g for 10 min. The postoperative samples were collected 2 to 34 days after surgery.
RNA libraries were prepared for sequencing using standard Illumina protocols,except rRNA depleted, RNAse R treated before library construction
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
rRNA depleted, RNAse R treated total RNA
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| Data processing |
Illumina Casava1.8.4 software used for basecalling.
Quality control was conducted by using fastQC, after quality control,fastx_trimmer was used to trim adaptor or bad quality sequence (10-120bp was kept), then published find_circ pipeline was used to predict circRNA candidates as the paper described
the function of intersect of bedtools was used to annotate the circRNA to circbase
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include mapped reads count by find_circ for each Sample
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| Submission date |
Nov 29, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shasha Li |
| E-mail(s) |
[email protected]
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| Phone |
01062798728
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| Organization name |
University of Michigan
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| Street address |
1109 Maiden Ln, ct apt 104
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| City |
ANN ARBOR |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE90741 |
Circular RNAs are super abundant in cervical tumor and plasma detected by high throughput microarray |
| GSE107472 |
Circular RNAs are super abundant in cervical tumor and plasma detected by high throughput microarray [RNA-Seq] |
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| Relations |
| BioSample |
SAMN08108308 |
| SRA |
SRX3428329 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2868038_17N_find_circ_result.txt.gz |
225.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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