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Sample GSM3815159 Query DataSets for GSM3815159
Status Public on Jul 25, 2019
Title ACA_6m_M_3
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics strain: UM-HET3
Sex: Male
age: 6 months
tissue: Liver
intervention: Acarbose
dose: 1000 ppm
intervention duration: 2 months
Treatment protocol Mice were kept on control diet (Purina 5LG6 for UM-HET3, GHRKO and Snell dwarf mice; 14% kcal protein, 76% kcal carbohydrate, and 10% kcal fat diet from Research Diets for C57BL/6J mice) or the same diet supplied with the certain compounds (acarbose, rapamycin, 17aE2, Protandim). In case of CR, Purina 5LG6 diet was restricted by 40%. In case of C57Bl/6J mice, controls were fed diet containing 0.86% w/w methionine whereas MR mice were fed the same diet but with 0.12% w/w methionine.
Extracted molecule total RNA
Extraction protocol After sacrifice, liver was removed and frozen on dry ice. RNA was extracted from liver tissues with PureLink RNA Mini Kit.
Sequencing libraries were prepared for sequencing using Illumina TruSeq RNA Sample Preparation v2 protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description PolyA RNA
processed data file: Interventions_assigned_reads.txt
Data processing HiSeq Control Software v2.2 was used for system control and base calling through an integrated primary analysis software RTA (Real Time Analysis. v1.18). The BCL (base calls) binary was converted into FASTQ utilizing Illumina package bcl2fastq (v1.8.4).
Quality filtering and adapter removal were performed using Trimmomatic version 0.32.
Reads were mapped to mm10 mouse genome using STAR (version 2.5.2b). Genes were counted via featureCounts (version 1.5).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Interventions_assigned_reads.txt: Tab-delimited text file includes gene counts for each sample.
 
Submission date May 24, 2019
Last update date Jul 25, 2019
Contact name Maxim Gerashchenko
E-mail(s) mgerashchenko@bwh.harvard.edu
Organization name Brigham and Women's Hospital
Department Medicine
Street address 77 Louis Pasteur Ave, NRB 435
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
 
Platform ID GPL24247
Series (2)
GSE131754 RNA sequencing of mouse hepatic response to lifespan-extending interventions
GSE131901 Identification and application of gene expression signatures associated with lifespan extension
Relations
BioSample SAMN11845974
SRA SRX5893270

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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