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Sample GSM1192682 Query DataSets for GSM1192682
Status Public on Jul 20, 2013
Title 2021_s_2
Sample type SRA
Source name serum
Organism Homo sapiens
Characteristics er status: pos
pr status: pos
her2 status: pos
inflammatory: N
Stage: 2
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 2021_s_2 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
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
BioSample SAMN02260862
SRA SRX326631

Supplementary file Size Download File type/resource
GSM1192682_2021_s_2_quantile_normal_serum_bc.txt.gz 6.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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