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Sample GSM2844572 Query DataSets for GSM2844572
Status Public on Feb 13, 2019
Title INS-1 S487D 1
Sample type SRA
 
Source name INS-1 S487D
Organism Rattus norvegicus
Characteristics cell line: INS-1
cell type: Rat insulinoma cells; Insulin secreting beta cell derived line
passages: 75-80
genotype/variation: overexpressing menin S487D mutant
Growth protocol INS-1 cells overexpressing menin S487A or S487D mutant were established by transduction with pMX-puro-Flag-Menin derived retroviruses, and cultured in RPMI1640 medium supplemented with 10% FBS, 10 mM HEPES buffer, 2 mM glutamine, 1 mM sodium pyruvate, 50 μM beta-mercaptoethanol and 1% Pen/Strep
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol reagent.The purity was assessed using the ND-1000 Nanodrop. Each RNA sample had an A260:A280 ratio above 1.8 and A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, USA) and each sample had the RINe above 7.0. mRNAs were isolated from Total RNA and fragmented to approximately 200bp. Subsequently, the collected mRNAs were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of TruSeq® RNA LT/HT Sample Prep Kit (Illumina, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description InsM-D-1_RPKM
Data processing base-calling:bcl2fastq(v2.17)
data filtrting step1:cutadapt(v1.8.1)
data filtrting step2:remove N bases(our program)
data filtrting step3:FASTQ quality filter:fastq_quality_filter(v0.0.13)
alignment genome:tophat(v2.0.13)
quantify gene count:gfold(V1.1.2)
Genome_build: NCBI rn6(GCF_000001895.5_Rnor_6.0)
Supplementary_files_format_and_content: abundance measurements
 
Submission date Nov 07, 2017
Last update date May 15, 2019
Contact name Bowen Xing
E-mail(s) bwxing@whu.edu.cn
Phone 86-13005411156
Organization name Shenzhen University
Street address Nanhai Street 3688
City Shenzhen
State/province Guangdong
ZIP/Postal code 518060
Country China
 
Platform ID GPL18694
Series (1)
GSE106653 GLP-1 signaling suppresses menin's transcriptional block by phosphorylation in beta cells
Relations
BioSample SAMN07998336
SRA SRX3372550

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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