|
| Status |
Public on Feb 12, 2019 |
| Title |
RKM-012-03 |
| 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 |
SAMN07960345 |
| SRA |
SRX3347499 |
