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Sample GSM2836985 Query DataSets for GSM2836985
Status Public on Feb 12, 2019
Title RKM-012-01
Sample type SRA
 
Source name Left ventricle (heart)
Organism Mus musculus
Characteristics strain: 129X1/SvJ
surgery: CKD
Sex: Male
Treatment protocol RNALater
Extracted molecule total RNA
Extraction protocol Hearts were removed, left ventricle isolated and preserved in RNALater, then frozen at -80C. Tissue was homogenized with beads in Qiazol and RNA isolated using RNAeasy Mini kit.
Libraries were prepared using the Illumina TruSeq mRNA protocol. Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell. Clustered flowcell was sequenced on an Illumina HiSeq 1000 in 100-base single-read reactions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1000
 
Description 165_Winterberg_FPKM_exprs.txt
Data processing Illumina Casava1.8.2 software used for basecalling and demultiplexing.
Reads were mapped to hg19 genome assembly with the STAR (v2.4.0f1) aligner args: --outFilterMultimapNmax 1 --outFilterType BySJout --outSJfilterReads Unique --sjdbGTFfile refGene.gtf --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Per sample annotated transcript models were quantitated with Cufflinks (v2.1.1) args: -G refGene.gtf
Sample transcript models were merged with Cuffmerge (v2.1.1)
FPKM (Fragments per kilobase of exon per million reads mapped) abundance estimates and differential expression was caluclated with Cuffdiff (v2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing FPKM for each sample (in columns) and each annotated transcript (in rows).
 
Submission date Oct 31, 2017
Last update date May 15, 2019
Contact name Gregory K Tharp
E-mail(s) gktharp@emory.edu
Phone 404-727-7797
Organization name Yerkes National Primate Research Center
Department Developmental and Cognitive Neuroscience
Lab Genomics Core
Street address 954 Gatewood Dr
City Atlanta
State/province GA
ZIP/Postal code 30329-4208
Country USA
 
Platform ID GPL15103
Series (1)
GSE106385 Gene expression profiles in experimental uremic cardiomyopathy.
Relations
BioSample SAMN07960347
SRA SRX3347497

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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