|
| Status |
Public on Sep 09, 2024 |
| Title |
ANM_122 |
| Sample type |
SRA |
| |
|
| Source name |
adjacent normal mucosa tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tumor stage: Not Applicable
tobacco smoking: Not Applicable
alcohol consumption: Not Applicable
sequencing type: Small RNA sequencing
|
| Treatment protocol |
Tumor and adjacent mormal mucosa tissues excised from LSCC patients after surgery were stored with RNAlater (Cat#AM7020，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA 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 |
| |
|
| Description |
P122
|
| Data processing |
Basecalls performed using Perl package developed by NOVOGENE
Contaminant reads from the fq file were removed and get the final clean reads. And then summarize the length distribution of these clean reads. Normally, length of small RNA is between 18nt and 30nt. The length distribution analysis is helpful to see the compositions of small RNA sample. For example, miRNA is normally 21nt or 22nt, siRNA is 24nt, and piRNA is 30nt.
The data is processed by the following steps: 1) Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table); 2) Getting rid of reads with 5' primer contaminants; 3) Getting rid of reads without 3' primer; 4) Getting rid of reads without the insert tag; 5) Getting rid of reads with poly A; 6) Getting rid of reads shorter than 18nt; 7) Summarize the length distribution of the clean reads.
Genome_build: hg19
Supplementary_files_format_and_content: 100_samples_miRNA_RPM.txt
|
| |
|
| Submission date |
Jun 05, 2019 |
| Last update date |
Sep 09, 2024 |
| Contact name |
Yongyan Wu |
| E-mail(s) |
[email protected]
|
| Organization name |
Shanxi Medical University
|
| Department |
Department of Otolaryngology Head & Neck Surgery, The First Hospital
|
| Lab |
Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer
|
| Street address |
No.85 South Jiefang Road, Taiyuan, Shanxi, China
|
| City |
Taiyuan |
| State/province |
Shanxi |
| ZIP/Postal code |
030001 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE132222 |
Small RNA sequencing of 50 laryngeal squamous cell carcinoma and paired adjacent normal tissues |
|
| Relations |
| BioSample |
SAMN11961206 |
| SRA |
SRX5974753 |
