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Sample GSM4146958 Query DataSets for GSM4146958
Status Public on Nov 01, 2022
Title db/db4
Sample type SRA
 
Source name islet cells
Organism Mus musculus
Characteristics strain/background: C57BL/6
genotype/variation: Lepr-/-
tissue: Pancreas
Extracted molecule total RNA
Extraction protocol Islets were isolated by collagenase digestion followed by purification on Histopaque (Sigma Aldrich, Germany) density gradient and used directly for RNA extraction.
The library for sequencing was constructed by removing ribosomal RNA from the total RNA.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description processed data file: all.counts.exp.txt
Data processing We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15, b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome.
Count counting.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: all.counts.exp.txt: Tab-delimited text file contains counts for each sample.
 
Submission date Nov 01, 2019
Last update date Nov 01, 2022
Contact name Li Xiong
E-mail(s) xiongl8@mail2.sysu.edu.cn
Phone 86-020-87755766-8450
Organization name The First Affiliated Hospital of Sun Yat-sen University
Department Department of Endocrinology
Street address 58 Zhongshan Road 2
City Guangzhou
State/province Guangdong
ZIP/Postal code 510080
Country China
 
Platform ID GPL21273
Series (1)
GSE139823 Next-generation sequencing facilitates quantitative analysis of wild type and diabetic db/db mice islets transcriptomes
Relations
BioSample SAMN13178333
SRA SRX7085331

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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