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Sample GSM3557556 Query DataSets for GSM3557556
Status Public on Sep 30, 2019
Title Aptamer-3
Sample type SRA
 
Source name Aptamer library
Organism Homo sapiens
Characteristics sample type: synthetic construct
molecule subtype: ssDNA
Extracted molecule genomic DNA
Extraction protocol ssDNA aptamers specific towards amyloid-β was selected by SELEX strategy from random aptamer library.
The amyloid-β specific ssDNA selected was cloned into pGMET vector by TA cloning strategy and sequenced.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model AB 5500xl Genetic Analyzer
 
Description The aptamer-3 processed from the forward and reverse scanned raw file
Data processing ssDNA sequence retrieval from sequence scanner software v2.0
ssDNA linear chain generation using Discover studio 2016 version
MD simulation of the linear ssDNA using Gromacs 2018 version and generation of 3D structure
MD simulation of aptamer against amyloid-β peptide
Supplementary_files_format_and_content: PDB files contains the three dimensional structure of the aptamer
 
Submission date Jan 09, 2019
Last update date Oct 01, 2019
Contact name Nikhil Maroli
E-mail(s) scinikhil@gmail.com
Phone 7200515138
Organization name DRDO BU CLS
Department Physics
Lab Computational Biology
Street address Bharathiar University
City Coimbatore
State/province TAMIL NADU
ZIP/Postal code 670691
Country India
 
Platform ID GPL16288
Series (1)
GSE124865 ssDNA aptamers against amyloid-β peptide as biomarker and inhibtor [SELEX]
Relations
BioSample SAMN10719282

Supplementary file Size Download File type/resource
GSM3557556_aptamer-3.txt.gz 94 b (ftp)(http) TXT
GSM3557556_aptamer3.pdb.gz 42.9 Kb (ftp)(http) PDB
GSM3557556_aptamer3_neg+2.fastq.gz 141 b (ftp)(http) FASTQ
GSM3557556_aptamer3_neg.fastq.gz 174 b (ftp)(http) FASTQ
Raw data provided as supplementary file
Processed data provided as supplementary file

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