|
Status |
Public on Sep 29, 2020 |
Title |
Young HFD 1 Methylseq |
Sample type |
SRA |
|
|
Source name |
Islets
|
Organism |
Mus musculus |
Characteristics |
age group: Young diet: high fat diet strain: C57BL/6 tissue: Islets age: 8-10 weeks 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 |
SAMN11890326 |
SRA |
SRX5930257 |