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| Status |
Public on Jan 01, 2019 |
| Title |
01_p53WT_Rep1 |
| Sample type |
SRA |
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| Source name |
Hind limb muscles
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Muscle
age: from 2 to 3 months old
genotype: p53 WT
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| Extracted molecule |
total RNA |
| Extraction protocol |
Muscles were removed, digested in collagenase and dispase, and isolated through flow cytometry using CD34 and alpha-7 integrin as positive markers and CD31, CD11b, CD45, and Sca-1 as negative markers; RNA isolation was performed using Qiagen RNaesy Micro kit (Cat. number: 74004); Libraries were preared using NEBNext Ultra II Directional RNA Library Prep kit for Illumina
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 NextSeq 500 |
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| Data processing |
Read data was processed in BasebeadSpace
Reads were alligned using STAR aligner with default settings
Differential expression analysis was performed using the Cufflinks Cuffdiff package
Pathway analysis was performed employing IPA, GSEA, and CE
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample
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| Submission date |
Dec 06, 2018 |
| Last update date |
Jan 02, 2019 |
| Contact name |
Francesca Boscolo |
| E-mail(s) |
[email protected]
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| Organization name |
UCSD
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| Department |
Reproductive Medicine
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| Lab |
Marianna Alperin
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92122 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE123423 |
Muscle stem cells give rise to rhabdomyosarcomas in severe model of Duchenne muscular dystrophy |
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| Relations |
| BioSample |
SAMN10526698 |
| SRA |
SRX5100216 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3502922_01_p53WT_Rep1.genes.fpkm_tracking.txt.gz |
643.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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