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Sample GSM1269355 Query DataSets for GSM1269355
Status Public on Dec 02, 2013
Title Mock transfection to HEK293, replicate 2
Sample type SRA
 
Source name HEK293 cells
Organism Homo sapiens
Characteristics transfection: Puc19(mock)
cell line: HEK293 cells
data type: RNA-seq fastq
Treatment protocol Cells were transfected with Lipofectamine 2000 (Invitrogen) and 100 nM miRNA duplex or pUC19, as described by the manufacturer.
Extracted molecule total RNA
Extraction protocol After 24 hours, cells were harvested, and RNA was extracted using TRI-reagent (Life Technologies).
After RNA isolation, poly(A)+ RNA was selected using oligo(dT) beads (Invitrogen). RNA-seq libraries were prepared by either a ligation-based approach, as previously described (Guo et al., 2010), or a dUTP-based approach (Bioo Scientific), according the manufacturer’s directions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description PolyA-selected RNAs
HEK293.exp.qn
Data processing Basecalls performed using CASAVA version 1.7
All RNA-seq data were mapped to the human reference genome (hg19) using Bowtie version 0.12.8 (Trapnell et al., 2009), allowing at most five genomic matches but choosing the best one (-n 1 -e 240 -m 5 --best --strata).
To measure expression level, we estimated both reads per kilobases per million reads (RPKM) values and reads per million reads (RPM) values based on RefSeq annotation (Aug-22-2011 version).
Quantile normalization was performed to reduce technical global bias of expressions between replicates and between wild type and transfected cells.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for pUC19_1, pUC19_2, miR-124_1, miR-124_2, miR-155_1, and miR-155_2
 
Submission date Nov 19, 2013
Last update date May 15, 2019
Contact name Jin-Wu Nam
E-mail(s) coya75@gmail.com
Organization name Hanyang University
Street address 222 Wangsimni Seongdong-gu
City Seoul
ZIP/Postal code 133-791
Country South Korea
 
Platform ID GPL9115
Series (2)
GSE52530 Global analyses of the effect of different cellular contexts on microRNA targeting (RNA-Seq)
GSE52531 Global analyses of the effect of different cellular contexts on microRNA targeting
Relations
BioSample SAMN02412862
SRA SRX379576

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

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