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Sample GSM3753979 Query DataSets for GSM3753979
Status Public on May 08, 2019
Title KO rep2
Sample type SRA
Source name beta cells
Organism Mus musculus
Characteristics strain: C57BL/6 x 129SV
age: 8 weeks
genotype: BetaRapKOGFP-/- without insulin pellet
Extracted molecule total RNA
Extraction protocol Islets were isolated, digested into single cells and FACS. RNA was harvested using RNeasy micro kit and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
Data processing Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
We used Hisat v2.0.4 to map the cleaned reads to the mouse mm10 reference genome.
After genome mapping, Stringtie v1.3.0 and TMM were used to caculate FPKM values.
Differentially expressed genes were identified using edgeR. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .
Submission date May 07, 2019
Last update date May 09, 2019
Contact name Qinglei Yin
Organization name Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine
Street address Ruijin Second Road No.197
City Shanghai
ZIP/Postal code 200025
Country China
Platform ID GPL21273
Series (1)
GSE130792 Raptor determines β-cell identity and plasticity independent of metabolic state
BioSample SAMN11585341
SRA SRX5799636

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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