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| Status |
Public on May 22, 2021 |
| Title |
ZYFR4 |
| Sample type |
SRA |
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| Source name |
plasma
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| Organism |
Homo sapiens |
| Characteristics |
diagnosis: healthy volunteer
sequencing protocol: small RNA-Seq
Stage: NOT applicable
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Norgen Plasma/Serum Circulating RNA Purification Mini Kit 51000 following the manufacturer's procedure
The total RNA quantity and purity were analyzed by Agilent Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 0.2-0.7 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA).
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
H group
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| Data processing |
Pre-processing of sequencing reads was performed by FastQC v. 0.10.1 for cleaning low quality sequences and by Cutadapt to trim adaptor sequences
Then processed clean reads with more than 17 nucleotides in length were aligned against human Genome (hg19) and miRBase 20 using Bowtie v. 0.12.7
Subsequently, identification and quantification of known and predicted potential miRNAs were finished by miRDeep v. 2.0.0.5
The significance of differential expression of miRNAs was determined with edgeR between healthy volunteers (H group) and PDAC patients (P group)
The results were expressed as mean ± SD. Differences between the groups were evaluated by analysis of variance, and post hoc analysis by the Tukey–Kramer test. A p Value less than 0.05 was considered statistically significant.
Genome_build: hg19
Supplementary_files_format_and_content: expression matrix, each column includes the expression value of each sample for miRNAs
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| Submission date |
May 22, 2018 |
| Last update date |
May 22, 2021 |
| Contact name |
Yifan Zhu |
| E-mail(s) |
celltransplant@163.com
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| Organization name |
Henan University Huaihe Hospital
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| Street address |
Xi Men Da Jie 115
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| City |
Kifeng |
| State/province |
Henan |
| ZIP/Postal code |
475000 |
| Country |
China |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE114778 |
Plasma miRNA expression profiling of pancreatic ductal adenocarcinoma patient, chronic pancreatitis patients and healthy population in China |
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| Relations |
| BioSample |
SAMN09238021 |
| SRA |
SRX4112897 |
| 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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