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| Status |
Public on Mar 09, 2016 |
| Title |
Dichloroacetate_rep1 |
| Sample type |
SRA |
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| Source name |
Dichloroacetate_rep1
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| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
tissue: Kidney
age: 8 weeks old
agent: Dichloroacetate
Sex: male
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy mini kits (Qiagen, Venlo, Netherlands) and treated with Turbo DNAse (Life Technologies, Carlsbad, CA). Libraries were prepared with a Truseq RNA Sample Preparation kit (Illumina, San Diego, CA).
Libraries were prepared with a Truseq RNA Sample Preparation kit (Illumina, San Diego, CA). RNA (1µg/sample) was fragmented and subject to first and second strand synthesis, 3' end adenylation, adaptor ligation and PCR amplification using the TruSeq Rapid SBS Kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
mouse was pre-treated intraperitoneally daily with DCA (250mg/kg) for 6 days
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| Data processing |
Trimmomatic (HEADCROP:14 LEADING:3 TRAILING:3 MINLEN:70)
and mapped to the mouse genome (GRC38.72) with tophat (--b2 –very sensitive)
Cufflinks and HTSeq (-a –s no)
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated from tophat bam files using bedtools and scaling to reads per 10 million. genomeCoverageBed -bg -split -scale $sc -ibam. Raw.txt: Counts for ensembl genes were generated in HTSeq. normalised.txt: normalised in DESeq (R) using estimateSizeFactors() and counts(normalized=TRUE)
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| Submission date |
Jun 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kristine Hardy |
| E-mail(s) |
kristine.hardy@anu.edu.au
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| Organization name |
University of Canberra
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| Lab |
Cytokine Gene Expression
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| Street address |
University of Canberra
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| City |
Bruce |
| State/province |
ACT |
| ZIP/Postal code |
0200 |
| Country |
Australia |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE69652 |
Dichloroacetate (DCA) prevents cisplatin-induced nephrotoxicity without compromising its anti-cancer properties. |
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| Relations |
| BioSample |
SAMN03764893 |
| SRA |
SRX1053426 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1705342_thKidney10.bedGraph.gz |
165.4 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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