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| Status |
Public on Oct 12, 2015 |
| Title |
blank32_S3 |
| Sample type |
SRA |
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| Source name |
heart, biventricle_blank
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
gender: male
tissue: heart, biventricle
age: 17 weeks
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| Extracted molecule |
total RNA |
| Extraction protocol |
Hearts were removed and ventricles were flash frozen in liquid nitrogen. RNA was harvested using Trizol reagent.
Ribosomal RNA depletion along with RNA fragmentation and conversion to paired-end, strand-specific Illumina sequencing libraries were performed with Illumina TruSeq preparation kits for strand-specific, paired-end RNA-Seq.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
rRNA-depleted total RNA
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| Data processing |
Illumina Casava1.8 software was used for basecalling. All 76 nt reads use phred33 quality scores.
Sequence reads were mapped to the transcriptome, defined by annotation based on the UCSC mm10 genes.gtf but with mitochondrial RNAs added, and associated bowtie2 index provided by Illumina iGenomes (incorporating the additional mitochondrial RNAs), using tophat v2.0.10 (fr-firststrand)
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the supplied gtf, based on UCSC mm10 genes.gtf but with mitochondrial RNAs added.
htseq-count data allows each user maximum flexibility in performing sample (library) depth normalization and differential gene expression using software such as DESeq or edgeR.
Additionally, we used Cufflinks v2.1 to calculate FPKM for each gene entry in each library. However, this was merely done for later graph display. Actual calculations of differential gene expression used htseq-count data as input to DESeq.
Genome_build: mm10
Supplementary_files_format_and_content: single tab-delimited text files include htseq-count values for each gene, or FPKM values for each gene.
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| Submission date |
Oct 11, 2015 |
| 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 |
GPL19057 |
| Series (1) |
| GSE73909 |
Chronic cardiac contractile dysfunction without hypertrophy does not provoke a compensatory transcriptional response |
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| Relations |
| SRA |
SRX1327904 |
| BioSample |
SAMN04160348 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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