 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 10, 2017 |
| Title |
P001_Nor miRNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
oral cavity
|
| Organism |
Homo sapiens |
| Characteristics |
patient: P001
disease: normal oral mucosa tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA, including miRNA, was isolated from premalignant, tumor or normal tissue samples by using TRIzol reagent (Invitrogen, Carlsbad, USA) according to the manufacturer’s instructions. The RNA for Next generation sequencing was evaluated with an Agilent 2100Bioanalyzer.
Libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The 50nt sequence tags from HiSeq sequencing will go through the data cleaning first, which includes getting rid of the low quality tags and several kinds of contaminants from the 50nt tags. Length distribution of clean tags are then summarized.
Afterwards, the standard bioinformatics analysis will annotate the clean tags into different categories and take those which can not be annotated to any category to predict the novel miRNA and base edit of potential known miRNA.
Genome_build: hg18
Supplementary_files_format_and_content: excel file includes the standard expression values of all samples and comparisons between each two samples of the same patient
|
| |
|
| Submission date |
Jul 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Wen Shi |
| E-mail(s) |
[email protected]
|
| Organization name |
Peking University School and Hospital of Stomatology
|
| Department |
Oral & Maxillofacial Surgery
|
| Street address |
Beijing, Haidian
|
| City |
Beijing |
| State/province |
Outside the US or Canada |
| ZIP/Postal code |
100191 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE70664 |
Integrated Profiling of mRNAs and microRNAs to Identify Potential Biomarkers for Oral Malignant Transformation [miRNA-Seq] |
| GSE70666 |
Integrated Profiling of mRNAs and microRNAs to Identify Potential Biomarkers for Oral Malignant Transformation |
|
| Relations |
| BioSample |
SAMN03852575 |
| SRA |
SRX1089879 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
