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Status |
Public on Mar 09, 2016 |
Title |
Dichloroacetate_rep2 |
Sample type |
SRA |
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Source name |
Dichloroacetate_rep2
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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 |
SAMN03764894 |
SRA |
SRX1053427 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1705343_thKidney11.bedGraph.gz |
133.7 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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