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| Status |
Public on Apr 21, 2015 |
| Title |
unstressed_PKCde-2KO_2 |
| Sample type |
SRA |
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| Source name |
Heart
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Whole heart
age (weeks): 12
Sex: M
genotype: combined knockout
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Hearts were removed and ventricular apexes were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per the Supplement of Matkovich SJ, Hu Y, Eschenbacher WH, Dorn LE, Dorn GW, II. Direct and indirect involvement of microRNA-499 in clinical and experimental cardiomyopathy. Circ Res. 2012;111:521-31.
non-strand-specific, single-end RNA-Seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
PKCdeKO8553
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| Data processing |
Illumina Casava1.6 and Casava1.8 software was used for basecalling; all 50 nt reads use phred33 quality scores, while all 42 nt reads use phred64 quality scores.
Sequence reads were mapped to the transcriptome, defined by the UCSC genes.gtf, for the mm10 genome and associated bowtie2 index provided by Illumina iGenomes, using tophat v2.0.10 .
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the UCSC mm10 genes.gtf.
We have not further normalized or manipulated the count data, preferring that each user perform sample (library) depth normalization using software such as DESeq or edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include htseq-count values for each gene
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| Submission date |
Oct 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Scot J Matkovich |
| E-mail(s) |
sjmatkovich@lilly.com
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| Organization name |
Eli Lilly and Company
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| Street address |
Lilly Corporate Center
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| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46285 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE62689 |
RNA-sequencing of unstressed and pressure-overloaded C57 mouse hearts with single or combined ablation of PKCdelta and PKCepsilon |
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| Relations |
| BioSample |
SAMN03142776 |
| SRA |
SRX741436 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1531489_PKCdeKO8553_HTSeq-count.txt.gz |
93.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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