|
| Status |
Public on Apr 10, 2014 |
| Title |
Tumor_tissue |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
disease status: breast cancer
cell type: tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated for each of tissue and serum samples and treated with Trizol reagent (Invitrogen) according to the manufacturer’s instructions. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent) with RIN number >7.0.
Approximately 1 ug of total pooled RNA were used to prepare small RNA library according to protocol of TruSeqâ„¢ Small RNA Sample Prep Kits (Illumina).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats were discarded followed the procedures as described in a previous study (Li et al., 2010).
Small RNA sequencing reads were aligned against 2,578 mature miRNA sequences from miRBase build 20 using bowtie.
Expression values are quantified by aggregating reads into counts and differential expression analysis is performed based on normalized deep-sequencing counts RPM values (NOISeq). In this study, we chose q = 0.8 for NOISeq to screen significant genes and log2FC as supplementary threshold.
Genome_build: human miRBase build 20
Supplementary_files_format_and_content: tab-delimited text files including RPM values for each sample.
|
| |
|
| Submission date |
Apr 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
ZhaoYun Li |
| E-mail(s) |
lzy8151@163.com
|
| Organization name |
Wenzhou Medical University
|
| Department |
School of Laboratory Medicine and Life Science
|
| Street address |
Chashan Higher Education Park
|
| City |
Wenzhou |
| State/province |
Zhejiang province |
| ZIP/Postal code |
318000 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE56614 |
Different miRNA expression profiles between human breast cancer turmors and serum |
|
| Relations |
| BioSample |
SAMN02721544 |
| SRA |
SRX513284 |
