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Sample GSM1705343 Query DataSets for GSM1705343
Status Public on Mar 09, 2016
Title Dichloroacetate_rep2
Sample type SRA
 
Source name Dichloroacetate_rep2
Organism Mus musculus
Characteristics strain: BALB/c
tissue: Kidney
age: 8 weeks old
agent: Dichloroacetate
Sex: male
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description mouse was pre-treated intraperitoneally daily with DCA (250mg/kg) for 6 days
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)
 
Submission date Jun 08, 2015
Last update date May 15, 2019
Contact name Kristine Hardy
E-mail(s) kristine.hardy@anu.edu.au
Organization name University of Canberra
Lab Cytokine Gene Expression
Street address University of Canberra
City Bruce
State/province ACT
ZIP/Postal code 0200
Country Australia
 
Platform ID GPL17021
Series (1)
GSE69652 Dichloroacetate (DCA) prevents cisplatin-induced nephrotoxicity without compromising its anti-cancer properties.
Relations
BioSample SAMN03764894
SRA SRX1053427

Supplementary file Size Download File type/resource
GSM1705343_thKidney11.bedGraph.gz 133.7 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA
Processed data provided as supplementary file

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