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Sample GSM3831312 Query DataSets for GSM3831312
Status Public on Sep 29, 2020
Title Old HFD 2 RNAseq
Sample type SRA
 
Source name Islets
Organism Mus musculus
Characteristics age group: Old
diet: high fat diet
strain: C57BL/6
tissue: Islets
age: 1 year
genotype: wild type
Treatment protocol Male mice 8 weeks or 52 weeks old were put on diets of 41% or 13.1 % kcal from fat diet for 1 week
Growth protocol C57/BL6J mice
Extracted molecule total RNA
Extraction protocol Islets were isolated, RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA sequencing libraries were prepared using the TruSeqStranded mRNA Library Preparation Kit in accordance with the manufacturer’s instructions (Illumina, Inc., San Diego, CA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description RNAseq
QC_statistics_to_deliver_old.txt
kallisto_est_count_matrix_old.txt
featureCounts_count_matrix_old.txt
DEseq2_results_HFD_SD_old.txt
HFD1YEAR2
Data processing >> RNA-Seq <<
Reads were aligned to the mm10 mouse reference using STAR aligner (v2.4.2a)
Quantification of genes annotated in Gencode vM5 was performed using featureCounts (v1.4.3)
Quantification of transcripts used Kalisto
QC were collected with Picard (v1.83) and RSeQC
Normalization of feature counts and differential expression analysis was done using the DESeq2 package
Genome_build: mm10
Supplementary_files_format_and_content: count and DEseq2 tab-delimited text files
>> Methyl-seq<<
Trim raw reads for quality Package: Trimmomatic Tool: illuminaclip
Map sequencing reads to mm10 Package: BSMAP Tool: BSMAP
Calculate percent methylation at CpGs Package: BSMAP Tool: methratio.py
Split by strand Package: BEDtools Tool: Split
Merge & sort by strand Package: BEDtools Tool: Merge
Remove Duplicates Package: Picard Tool: MarkDuplicates
Merge strands Package: BEDtools Tool: Merge
Filter for properly paired reads Package: Picard Tool: MarkDuplicates
Clip overlapping reads Package: BSMAP Tool: methratio.py
Genome_build: mm10
Supplementary_files_format_and_content: compressed tab-delimited methyl call txt files
 
Submission date May 29, 2019
Last update date Sep 29, 2020
Contact name Donald K Scott
E-mail(s) donald.scott@mssm.edu
Phone 4129926061
Organization name MSSM
Department Diabetes Obesity and Metabolism Institute
Lab Scott
Street address 1428 Madison Avenue
City New York
State/province New York
ZIP/Postal code 10029
Country USA
 
Platform ID GPL17021
Series (1)
GSE131941 Myc is required for adaptive beta cell replication in young mice but is not sufficient in one year old mice fed with a high fat
Relations
BioSample SAMN11890333
SRA SRX5930250

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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