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Sample GSM1246704 Query DataSets for GSM1246704
Status Public on Oct 22, 2013
Title Lung Cancer Cell Line H460
Sample type SRA
Source name Total RNA from H460 cells
Organism Homo sapiens
Characteristics cell line: H460
Treatment protocol Not Applicable
Growth protocol Cells were cultured in RPMI-1640, supplemented with 10% FBS and 1X Penicillin/Streptomycin. Xenografts were grown by subcutaneous injection of two million trypsin-dissociated tumor cells into non-obese diabetic/severe combinted immunodeficient mice.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from confluent cell lines or fresh-frozen xenograft tissues using Trizol reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer's instructions, followed by Dnase I treatment (Life Technologies) and purification using the Qiagen RNeasey kit (Qiagen, Venlo, Netherlands). RNA quantity and quality was assessed using the Qubit Fluorometer (Life Technologies), NanoDrop 1000 (Nanodrop Technologies, Wilmington, DE, USA), and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Five micrograms of total RNA was fractionated using the flashPAGETM fractionator system (Life Technologies) and small RNAs (~<40nt) were recovered by ethanol precipitation. Small RNA enrichment was confirmed using the small RNA Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent).
Libraries were prepared from fractionated small RNA samples as per Illumina TruSeq Small RNA protocol (version D) (Illumina, San Diego, CA, USA).
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
Data processing Base-calling was performed using CASAVA v1.8.2. Short read sequences were output in FASTQ format with corresponding base quality scores. Quality control of the raw sequences from each sequenced library was investigated using FastQC v0.9.1 to check for homopolymers, adapters, and distribution of base quality.  The raw data was initially filtered for reads containing ambiguous base calls, which did not meet the Illumina chastity filter based on quality measures. 
The remaining reads were trimmed for adapters and mapped to the miRBase v16 mature miRNA reference using Novocraft's Novoalign v2.07.14.
The summarized count data was loaded into the R statistical environment (v2.14.0) and normalized by linear regression using the median count value of each miRNA across the samples as reference.
Genome_build: miRBase version 16.0
Supplementary_files_format_and_content: Tab-delimited text file contains linear-normalized counts for each aligned microRNA.
Submission date Oct 21, 2013
Last update date May 15, 2019
Contact name Shirley Tam
Organization name Ontario Institute for Cancer Research
Department Genome Technologies
Street address 661 University Avenue, Suite 510, MaRS Building, West Tower
City Toronto
State/province Ontario
ZIP/Postal code M5G 0A3
Country Canada
Platform ID GPL16791
Series (2)
GSE51507 Comparison of microRNA Profiling Platforms (HTS)
GSE51508 Comparison of microRNA Profiling Platforms
BioSample SAMN02378769
SRA SRX366065

Supplementary file Size Download File type/resource
GSM1246704_DMIE_0002_Lu_C_SE_146_SM_AGTCAAN_L001_R1_001.txt.gz 4.7 Kb (ftp)(http) TXT
GSM1246704_DMIE_0002_Lu_C_SE_146_SM_AGTCAAN_L002_R1_001.txt.gz 4.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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