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| Status |
Public on Feb 01, 2018 |
| Title |
axolotl_sham_12_3 |
| Sample type |
SRA |
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| Source name |
Heart ventricles
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| Organism |
Ambystoma mexicanum |
| Characteristics |
tissue: Heart ventricles
strain: wild-type, black
timepoint: 12 hours post resection
surgical treatment: sham surgery
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| Treatment protocol |
neonatal CD1 mice, adult axoltol and zebrafish are subjected to apical resection to remove ~15% of the ventricular mass. Sham surgeries are performed as control.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from the lower half of the ventricle of resected and sham hearts was isolated using Trizol at three different time points: 12, 24, and 48 hours post-surgery. Three biological replicates were used for each time point and condition in each species. For neonatal mice and axolotls, each replicate represents myocardium from a single animal. Due to the smaller size of the zebrafish, each biological replicate represents three pooled tissue samples. Poly-adenylated mRNA was isolated using the Wafergen #400047 protocol.
RNA-sequencing libraries were prepared with the IntegenX Directional PrepX mRNA kit. Paired-end (50 base pairs) sequencing was performed using an Illumina HiSeq 2500.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
axolotl_sham_12_3
A12_s3
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| Data processing |
Tophat 2 was used to align paired-end sequence reads to the GRCm30 genome for mouse and GRCz10 genome for zebrafish29
For mouse and zebrafish samples, Cufflinks was used to estimate gene expression levels in aligned reads and the resulting data was processed with Cuffdiff to identify differentially expressed genes between resected and sham groups at each time point and species
Trinity was used to produce a de novo transcriptome for Axolotl.
RSEM was used to analyzed Axolotl data.
Genome_build: GRCm30 (mouse), GRCz10 (zebrafish); FASTA for Axolotl transcripts is available on the series record.
Supplementary_files_format_and_content: text files with expression values (TPM, FPKM)
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| Submission date |
Dec 24, 2017 |
| Last update date |
Feb 09, 2018 |
| Contact name |
Niranjana Natarajan |
| E-mail(s) |
niranjana_natarajan@harvard.edu
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| Organization name |
Harvard University
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| Street address |
7 Divinity Avenue
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| City |
Cambridge |
| ZIP/Postal code |
02138 |
| Country |
USA |
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| Platform ID |
GPL22800 |
| Series (1) |
| GSE108493 |
RNA seq analysis of regenerating hearts from three models of successful cardiac regeneration |
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| Relations |
| SRA |
SRX3509930 |
| BioSample |
SAMN08242809 |
| 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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