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Sample GSM4667087

Query DataSets for GSM4667087

Status

Public on Jul 11, 2020

Title

3MK9

Sample type

SRA

Source name

kidney

Organism

Mus musculus

Characteristics

strain: C57BL/6
tissue: kidney
Sex: male
age: 3 month old

Growth protocol

The mice were housed at 25°C and fed standard rodent chow and tap water.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 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 the left RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the Truseq Stranded Total RNA HT Sample Prep Kit (Illumina, San Diego, USA).

Library strategy

ncRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina HiSeq 4000

Data processing

Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using TopHat2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion and CIRCExplorer2. All samples were generated unique circular RNAs.
Genome_build: Mus_musculus Ensembl relaese-88
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each isoforms

Submission date

Jul 10, 2020

Last update date

Jul 11, 2020

Contact name

Fan Fan Gao

E-mail(s)

[email protected]

Phone

15891722241

Organization name

the First Affiliated Hospital of Xi’an Jiaotong University