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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 18, 2022 |
| Title |
DG1Skin |
| Sample type |
SRA |
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| Source name |
Skin
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| Organism |
Octodon degus |
| Characteristics |
tissue: Skin
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| Treatment protocol |
No treatment
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| Growth protocol |
Wild caught
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were extracted from recently (<12hr) deceased or euthanized animals and flash frozen in liquid nitrogen. Animals not euthanized in lab were kept at 4°C and processed within 12hr of death. Frozen tissues were pulverized using a Cell Crusher piston chilled with liquid nitrogen to produce uniform powdered tissue. Approximately 30mg of frozen tissue powder was used for Trizol RNA extraction. Contaminating DNA was removed from RNA samples using Purelink DNase kit along with Purelink RNA columns. Purified RNA quality was checked using agarose gel examination for rRNA integrity and Qubit analysis
For RNAseq, the RNA samples were processed with the Illumina TruSeq stranded total RNA RiboZero Gold kit and then subjected to Illumina HiSeq 4000 paired-end 150bp sequencing; For MeDIP, genomic DNA samples were processed using the NEBNext UltraII DNA Library Prep kit.
Ribo-depletion for RNAseq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Data processing |
raw fastq reads files were cleaned by Trimmomatic-0.36
gene expression (reads counts) were calculated by salmon 1.4.0
Supplementary_files_format_and_content: gene expression
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| Submission date |
Dec 13, 2021 |
| Last update date |
May 18, 2022 |
| Contact name |
jinlong lu |
| E-mail(s) |
bioyuyang@hotmail.com
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| Phone |
5853098469
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| Organization name |
University of Rochester
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| Lab |
Gorbunova & Seluanov Labs
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| Street address |
213 Hutchinson Hall
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| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14627 |
| Country |
USA |
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| Platform ID |
GPL31074 |
| Series (1) |
| GSE190756 |
Comparative transcriptomics reveals circadian and pluripotency networks as two pillars of longevity regulation |
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| Relations |
| BioSample |
SAMN23970837 |
| SRA |
SRX13395970 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5730614_sort.DG1Skin.ht2.DEGUS.exp.salmon.txt.gz |
199.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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