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Sample GSM4929732 Query DataSets for GSM4929732
Status Public on Nov 23, 2023
Title SHAM1
Sample type SRA
 
Source name Diabetic rats after sham operation
Organism Rattus norvegicus
Characteristics strain: wistar
tissue: liver
group: Diabetic rats after sham operation
genotype: wild type
Treatment protocol Then the eligible animals were randomly divided into two body weight-matched groups (SG and SHAM) .
Growth protocol Cohorts of rats used in the study received a 60 kcal% saturated high-fat diet (HFD) (60% of calories as fat) for four weeks and followed a single intraperitoneal injection with streptozotocin (35 mg/kg in sodium citrate buffer) after 16h of fasting to induce DM. Three days after the STZ administration, rats with fasting blood glucose consistently exceeded 16.7 mmol/L were considered as promising diabetic model.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0. Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, USA). Then left RNAs were treated with Rnase R (Epicentre Inc, Madison, WI, USA) to remove linear RNAs and to enrich circRNAs. After removing ribosomal and linear RNAs, the enriched circRNAs were fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA,which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP.. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single-or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs,The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Hiseq 4000 (LC Bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 4000
 
Data processing Cutadapt-1.9 (https://cutadapt.readthedocs.io/en/stable/) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Tophat-2.0.10(http://ccb.jhu.edu/software/tophat/index.shtml) to map reads to the genome, Ensembl v96(command line: tophat2 –o outputFolder --transcriptomeindex=genome.fa --phred64-quals R1.fastq.gz R2.fastq.gz).
CIRCExlorer2 v2-2.2.6(http://yanglab.github.io/CIRCexplorer/) and CIRIv2.0.2(https://sourceforge.net/projects/ciri/) were used to identified circRNA.
circRNA was quantified and normalized according to SRPBM = number of circular reads/ (number of mapped reads (units in billion) * read length).
Genome_build: Rnor_6.0.96
Supplementary_files_format_and_content: tab-delimited text files include circRNA srpbm values for each Sample
 
Submission date Nov 23, 2020
Last update date Nov 23, 2023
Contact name Linchuan Li
E-mail(s) linchuanlee@hotmail.com
Organization name Shandong University
Street address 16766# Jingshi Road
City Jinan
State/province Shandong
ZIP/Postal code 250000
Country China
 
Platform ID GPL22396
Series (2)
GSE162013 Next generation sequencing of circular RNAs in diabetes mellitus rats after sleeve gastrectomy
GSE162022 Next generation sequencing of circular and lnc RNAs in diabetes mellitus rats after sleeve gastrectomy
Relations
BioSample SAMN16874201
SRA SRX9556881

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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