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| Status |
Public on May 14, 2013 |
| Title |
Sham2 |
| Sample type |
SRA |
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| Source name |
heart (left ventricle)
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: heart (left ventricle)
developmental stage: adult
strain: Sprague-Dawley
rna isolation method: Qiagen Rneasy Fibrous Tissue Kit
surgical procedure: Sham (identical to TAC procedure without constriction)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Hearts were removed, stored in RNAlater, and RNA was harvested using either Trizol reagent or Qiagen Rneasy Fibrous Tissue Kit (as noted in Samples section). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
Illumina Casava1.7 software used for basecalling for Samples1-4, 7 and 8 (and then converted to maq ill2sanger), Casava1.8 used for Samples 5, 6, and 9.
Sequenced reads were mapped to rn4 whole genome using tophat v1.3.1 with parameters with butterfly search option (--butterfly) and individual insert sizes specified (-r). Insert size was estimated from highest peak on Agilent DNA High Sensitivity electropherogram
Transript models were built for each sample using Cufflinks v1.0.3 with multiread correction (-u), upper quartile normalization (-N), cDNA fragment bias correction (-b with ensembl rn4 fasta reference), and the reference transcript annotation was used to guide assembly (-g). Transcript models were merged using cuffcompare with genomic sequence (-s) with refernce GTF (-r) and transcripts were reduced with (-R) by only keeping transcripts that overlapped with input loci. Differential expression between the three groups (TAC, sham, and fetal) and statistical significance was calculated with cuffdiff using upper quartile normalization (-N).
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
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| Submission date |
Nov 20, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Elizabeth Ames |
| Organization name |
University of Virginia
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| Department |
Biomedical Engineering
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| Lab |
Cardiac Biomechanic
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| Street address |
Box 800759, Health System
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| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22903 |
| Country |
USA |
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| Platform ID |
GPL10669 |
| Series (1) |
| GSE42411 |
Whole-transcriptome analysis identifies re-expression of fetal splice variants in cardiac hypertrophy |
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| Relations |
| SRA |
SRX205344 |
| BioSample |
SAMN01817927 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1039512_Sham6.genes.txt.gz |
774.9 Kb |
(ftp)(http) |
TXT |
| GSM1039512_Sham6.isoforms.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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