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Sample GSM2470988 Query DataSets for GSM2470988
Status Public on Aug 23, 2017
Title Plasmid_replicate1
Sample type SRA
Source name plasmid DNA
Organism synthetic construct
Characteristics sample type: Input plasmid library before transfection
Extracted molecule other
Extraction protocol 1ng plasmid library was amplified with PCR using primers AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT (universal primer) and CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTCAGACGTG (Illumina index 7 primer). The PCR products were purified using 0.8 X Agencourt AMPureXP DNA beads, quantified with Agilent DNA1000 Chip (Agilent, 5067-1504) and then sequenced on a HiSeq 2500 (Illumina) with 250bp pair-end sequencing.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
Data processing Illumina HCS 2.2.68 used for basecalling.
The raw reads were mapped to human reference genome hg19 using BWA version 0.7.12-r1039 with the parameters:bwa mem -M
Fragments of a size ranging from 400bp to 600 bp and overlapped with at least one selected SNP were kept for further analysis using an in-house perl script.
Count the number of fragments overlapped with each SNP site by an in-house perl script.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files including the counts of fragments overlapped with each SNP site for each Sample.
Submission date Jan 27, 2017
Last update date May 15, 2019
Contact name Xiaoyue Wang
Organization name Chinese Academy of Medical Sciences
Street address 5 Dongdansantiao, Dongcheng District
City Beijing
ZIP/Postal code 100005
Country China
Platform ID GPL19604
Series (1)
GSE94140 Systematic Identification of Regulatory Variants Associated with Cancer Risk
BioSample SAMN06276397
SRA SRX2523183

Supplementary file Size Download File type/resource
GSM2470988_2nd_input_fragment_counts.txt.gz 64.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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