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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 11, 2021 |
| Title |
TAC - Fat 60 - 3 |
| Sample type |
SRA |
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| Source name |
heart tissue
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J - 12-wk-old
diet: high-fat
surgery: transverse aortic constriction
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Mini Kit (Qiagen, cat# 74104)
2 ug of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Hearts isolated 1 week after surgery
4242Rutgers_hiFat-DESeq2_results_allgenes.xlsx
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| Data processing |
Illumina NextSeq 500
Alignement with the genome using STAR (Spliced Transcripts Alignment to a Reference) algorithm
Read pairs that had both ends aligned were counted, and those with at least 25 bp overlapping bases in a fragment were assigned
Gene annotations were obtained from Subread package. Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-930, doi:10.1093/bioinformatics/btt656 (2014).
Differential genes were detected by DESeq2 at 10%FDR (adjusted p-value). Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15, 550, doi:10.1186/s13059-014-0550-8 (2014).
Genome_build: mm10
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| Submission date |
Jan 19, 2021 |
| Last update date |
May 11, 2021 |
| Contact name |
Maha Abdellatif |
| E-mail(s) |
abdellma@njms.rutgers.edu
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| Phone |
9739721254
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| Organization name |
Rutgers-University
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| Department |
Cell Biology and Molecular Medicine
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| Street address |
185 S. Orange Ave.
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| City |
Newark |
| State/province |
NJ |
| ZIP/Postal code |
07103 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE165085 |
Diet- and stress-induced changes of RNA in mouse heart |
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| Relations |
| BioSample |
SAMN17379900 |
| SRA |
SRX9895378 |
| 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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