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| Status |
Public on Feb 22, 2019 |
| Title |
Loxp/loxp rep5 |
| Sample type |
SRA |
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| Source name |
heart
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
organ: heart
age: 13-week-old
genotype: Loxp/Loxp,Cre-
gender: male
experiment: B
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| Extracted molecule |
total RNA |
| Extraction protocol |
heart were removed, flash frozen on dry ice, and RNA was harvested using Qiagen Fibrous RNAeasy kit.
Experiment A was constructed with Ion Total RNA-Seq Kit v2 and Experiment B was prepared with Illumina TruSeq RNA Stranded mRNA HT Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
WT_m_1800
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| Data processing |
Experiment A was aligned to mm10 by the Ion Torrent Suite and Experiment B was aligned to the reference genome mm10 by STAR v2.6.0c
Experiment A was quantified by ENSEMBL annotations and normalized using Deseq algorithm by the StrandNGS program
Experiment B was qunatified using ENSEMBLv93 annotations and normalized at the gene-level, using a resampling strategy, the code is available at https://github.com/itmat/Normalization (-v0.8.5b-beta)
Genome_build: mm10
Supplementary_files_format_and_content: For experiment A, tab-delimited text file with transcript-level read counts. For experiment B, tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.
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| Submission date |
Jan 24, 2019 |
| Last update date |
Feb 22, 2019 |
| Contact name |
Jeffrey Field |
| E-mail(s) |
[email protected]
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| Organization name |
University of Pennsylvania
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| Department |
Pharmacology
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| Street address |
1313 BRB II/III U
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104-6084 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE125603 |
Targeting MRTF/SRF in CAP2-dependent dilated cardiomyopathy delays disease onset |
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| Relations |
| BioSample |
SAMN10819232 |
| SRA |
SRX5291443 |
| 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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