|
| Status |
Public on Sep 29, 2020 |
| Title |
Young RD 2 RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Islets
|
| Organism |
Mus musculus |
| Characteristics |
age group: Young
diet: standard 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 |
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_young.txt
kallisto_est_count_matrix_young.txt
featureCounts_count_matrix_young.txt
DEseq2_results_HFD_SD_young.txt
SD1WK2
|
| 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 |
SAMN11890343 |
| SRA |
SRX5930240 |
