|
| Status |
Public on Jul 20, 2013 |
| Title |
PN01679_s_8 |
| Sample type |
SRA |
| |
|
| Source name |
serum
|
| Organism |
Homo sapiens |
| Characteristics |
er status: pos
pr status: neg
her2 status: neg
inflammatory: N
Stage: 3
relapse: N
molecule subtype: miRNA
|
| Treatment protocol |
Pre-treatment sera from BC patients were used.
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIZOL LS reagent (Invitrogen) was used to extract total RNA from ~1.5 ml of serum, as described in the manufacturer’s protocol. RNA pellet was dissolved in 10 μl of RNase-free water, and subjected to library construction and deep sequencing.
Each serum sample was independently subjected to library preparation and deep sequencing. All small RNAs of 15–52 nts were selected and sequenced using the Solexa system, following the manufacturer’s protocol (Illumina Inc., San Diego, CA). Library preparation, as well as cluster generation and deep sequencing, was performed according to the 5' ligation-dependent (5′ monophosphate-dependent) manufacturer’s protocol (Digital Gene Expression for small RNA; Illumina). For each sample, 5 μl of total RNA extracted from serum was used for small RNA library preparation. Small RNAs were size-selected between 17 and 52 nt according to the single-stranded DNA marker in the small RNA sequencing kit (Illumina). The library was quantified using picoGreen and qPCR. Sequencing was performed on a Genome Analyzer IIx (Illumina), and image processing and base calling were conducted using Illumina’s pipeline.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PN01679_s_8 serum
|
| Data processing |
Sequenced reads from Solexa were first mapped onto human genome version hg18 using novoalign software and the expression level of mature miRNAs in the miRBase human miRNA database v15 was summarized.
Quantile normalization was applied to the counts data
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each miRNA
|
| |
|
| Submission date |
Jul 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiwei Wu |
| E-mail(s) |
xwu@coh.org
|
| Organization name |
Beckman Research Institute
|
| Department |
Molecular and Cellular Biology
|
| Lab |
Integrative Genomics Core
|
| Street address |
1500 E Duarte Rd
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE49035 |
De novo sequencing of circulating microRNAs in locally advanced breast cancer |
|
| Relations |
| BioSample |
SAMN02260831 |
| SRA |
SRX326612 |
