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| Status |
Public on Oct 22, 2013 |
| Title |
Lung Xenograft A549 |
| Sample type |
SRA |
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| Source name |
Total RNA from A549 xenograft
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| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
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| Treatment protocol |
Not Applicable
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| 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.
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| 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.
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| Submission date |
Oct 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Shirley Tam |
| E-mail(s) |
shirley.tam@mail.utoronto.ca
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| Organization name |
Ontario Institute for Cancer Research
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| Department |
Genome Technologies
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| Street address |
661 University Avenue, Suite 510, MaRS Building, West Tower
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| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A3 |
| Country |
Canada |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE51507 |
Comparison of microRNA Profiling Platforms (HTS) |
| GSE51508 |
Comparison of microRNA Profiling Platforms |
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| Relations |
| BioSample |
SAMN02378764 |
| SRA |
SRX366064 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1246703_DMIE_0001_Lu_X_SE_146_SM_GTCCGCN_L001_R1_001.txt.gz |
4.5 Kb |
(ftp)(http) |
TXT |
| GSM1246703_DMIE_0001_Lu_X_SE_146_SM_GTCCGCN_L002_R1_001.txt.gz |
4.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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