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Sample GSM3831325 Query DataSets for GSM3831325
Status Public on Sep 29, 2020
Title Old SD 3 Methylseq
Sample type SRA
 
Source name Islets
Organism Mus musculus
Characteristics age group: Old
diet: standard 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 genomic DNA
Extraction protocol Islets were isolated, DNA was isolated,
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina MiSeq
 
Description Methylseq
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 GPL16417
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 SAMN11890349
SRA SRX5930263

Supplementary file Size Download File type/resource
GSM3831325_methylcall.CpG.1Y_1wk_RD_3.1x.txt.gz 2.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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