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Sample GSM5732021 Query DataSets for GSM5732021
Status Public on Dec 15, 2022
Title Islets MUT4_1201
Sample type SRA
 
Source name Islets
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Islets
age: 8 weeks old
genotype: Ngn3-Cre; Ctnna1 flox/flox
Extracted molecule total RNA
Extraction protocol Islet were isolated, disrupted and lyzed in RLT buffer. RNA was harvested using RNeasy kit (Quiagen).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Illumina bcl2fastq v2.18.0.12 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR 2.6.0.a with default parameters
The HTSeq software (v.0.6.0) was applied to generate the count matrix, with default parameters. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR 3.28.1.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
 
Submission date Dec 13, 2021
Last update date Dec 15, 2022
Contact name Steven T Rosen
Organization name City of Hope
Department Department of Hematology and Hematopoietic Cell Transplantation
Street address 1500 E. Duarte Road
City Duarte
State/province CA
ZIP/Postal code 91010
Country USA
 
Platform ID GPL17021
Series (1)
GSE190788 Investigating the role of cell adhesion molecule alpha-catenin during islet development
Relations
BioSample SAMN24006326
SRA SRX13397604

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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