NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1842530 Query DataSets for GSM1842530
Status Public on Dec 31, 2020
Title plasma_granuloma_9
Sample type SRA
 
Source name plasma
Organism Homo sapiens
Characteristics tumor: granuloma
Growth protocol EDTA Plasma samples stored at −80°C from 38 individuals with benign IPNs. Plasma from 7 early stage adenocarcinoma patients and 10 granuloma cases were used for biomarker discovery by next generation sequencing (NGS)
Extracted molecule total RNA
Extraction protocol 50 µl serum was mixed well with 12.6 µl ExoQuick exosome isolation solution, and incubated on ice for 30 min. Then the samples were centrifuged at 1000 g for 30 min at 4°C. The pellet was washed wish 1X DPBS and resuspended in 50 µl 1X DPBS. 20 µl samples were loaded onto the nanochip and incubated at 37ºC for 2 h. On each chip, two wells with 1XDPBS were used as negative control.
The NextGen sequencing libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencing kit (New England Biolabs). The 3’ and 5’ adapters and the reverse transcription primer were diluted in nuclease-free water to concentrations specified by the kit. The adapter sequences were ligated to the 3’ and 5’ ends of the RNA isolated from 100 μL of plasma using T4 RNA ligase. Ligation reactions were performed overnight at 16oC to maximize efficiency. cDNA was then transcribed from the ligation product followed by PCR amplification with a unique barcode sequence for each sample. The fragment size of about 150 nts, was then extracted and purified from an acrylamide gel. The final purified and barcoded libraries were then pooled in equal molar for single-end 50 nt sequencing run using an Illumina HiSeq2500 instrument.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
 
Description plasma_granuloma_DB331_L1_R1
Data processing Basecalls performed using CASAVA version X.X.X
The reads were processed by trimming off the adaptor sequences and removing low quality sequences, polyA sequences and adaptor-only sequences. We used a “map and remove” strategy to map the sequence reads to various databases as described.
The processed sequences were first screened against known human microRNA, human transcripts, followed by human genomic sequence. To get mapping results, the alignment tool Blast was used to search microRNA and Bowtie was used to search other large databases.
For the endogenous sequence mapping, except microRNA, we applied three different levels of error tolerance: 0 mismatch, 1 and 2 mismatches. Due to the high sequence similarity for microRNA, we did not allow any sequence mismatch. After normalizing the mapping results with total number of reads, the number of reads mapped to a specific transcript should be proportional to its concentration in circulation.
Genome_build: miRBase21
Supplementary_files_format_and_content: tab-delimted text files include RPM values for each sample.
 
Submission date Aug 03, 2015
Last update date Dec 31, 2020
Contact name Kai Wang
E-mail(s) kwang@systemsbiology.org
Organization name Institute for Systems Biology
Street address 401 Terry Ave N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL16791
Series (1)
GSE71661 TTF1 and TKTL1 mRNAs in Extracellular Vesicles as a Blood Biomarker for Lung Adenocarcinoma
Relations
BioSample SAMN03952593
SRA SRX1130459

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap