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Sample GSM5730655 Query DataSets for GSM5730655
Status Public on May 18, 2022
Title DM6Liver
Sample type SRA
 
Source name Liver
Organism Peromyscus maniculatus
Characteristics tissue: Liver
Treatment protocol No treatment
Growth protocol Wild caught
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 550
 
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
 
Submission date Dec 13, 2021
Last update date May 18, 2022
Contact name jinlong lu
E-mail(s) bioyuyang@hotmail.com
Phone 5853098469
Organization name University of Rochester
Lab Gorbunova & Seluanov Labs
Street address 213 Hutchinson Hall
City Rochester
State/province NY
ZIP/Postal code 14627
Country USA
 
Platform ID GPL31075
Series (1)
GSE190756 Comparative transcriptomics reveals circadian and pluripotency networks as two pillars of longevity regulation
Relations
BioSample SAMN23970547
SRA SRX13395979

Supplementary file Size Download File type/resource
GSM5730655_sort.DM6Liver.ht2.DM.exp.salmon.txt.gz 143.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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