|
| Status |
Public on Jul 25, 2019 |
| Title |
CON_6m_M_2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: UM-HET3
Sex: Male
age: 6 months
tissue: Liver
intervention: Control
dose: -
intervention duration: -
|
| 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 |
SAMN11846010 |
| SRA |
SRX5893305 |
