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Sample GSM5694321

Query DataSets for GSM5694321

Status

Public on Nov 30, 2021

Title

Lung tissues 1

Sample type

SRA

Source name

Lung tissues

Organism

Rattus norvegicus

Characteristics

strain: SD
tissue: Lung
treated: Untreated
Sex: male

Treatment protocol

The rats in the PVOD group were injected intraperitoneally with mitomycin-C (GC12353, GLPBIO, USA) on the first day (2 mg/kg) and eighth days (2 mg/kg),

Growth protocol

the rats in the control group were injected intraperitoneally with phosphate buffer saline at the same doses and times.

Extracted molecule

total RNA

Extraction protocol

We removed the bronchi, pulmonary arteriovenous and enclosed lung tissue near the right hilum, and tried to take the lung tissue near the periphery for detection under a dissecting microscope. Finally, pulmonary veins and lung tissue were collected and placed in liquid nitrogen tanks for storage before RNA extraction and western blot
Libraries were prepared according to Illumina's instructions. The main steps for the preparation of miRNA libraries as follows. Firstly, pulmonary vein and lung tissues total RNA was isolated using Trizol reagent (CW0580S, CWBIO, China) and RNA quality was determined by using a Qubit RNA kit (Life Technologies Corporation, CA, USA). Secondly, the 3' end of RNA was spliced using T4 RNA ligase 2 (0511412, NEB, Herts, UK). Thirdly, RT primer was added to the 3' -end ligands for reverse transcription primer hybridization. Fourthly, the 5' end of RNA was spliced using T4 RNA ligase 1 (0011309, NEB, Herts, UK). Then, the cDNA strand of the linker was obtained by reverse transcription. Next, the reverse transcription was amplified by PCR. Finally, the cDNA purity was verified with 12% PAGE gelelectrophoresis, and PCR product bands of about 140-150 bp were recovered. We used a Qubit DNA kit to quantify DNA, and then used for library preparation and Illumina sequencing. Sequencing and analysis of the transcriptome of the samples were performed at Sangon biotech Co., Ltd (Shanghai, China).

Library strategy

miRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

NextSeq 550

Description

Data processing

MirDeep2 v 2.0.0.8 software was used to predict new miRNA
The software used for GO and KEGG enrichment analysis was clusterProfiler 3.4.4
network graph drawing software was igraph 1.1.2
Raw sequencing data were assessed for quality by FastQC v0.11.5, cutadapt 1.14 was used to remove connectors, Trimmomatic v 0.36 was used to remove low quality bases at both ends, and reads 3.4.1 were filtered
Genome_build: mm9
Supplementary_files_format_and_content: RPM
Supplementary_files_format_and_content: count

Submission date

Nov 18, 2021

Last update date

Nov 30, 2021

Contact name

Qing Song

E-mail(s)

[email protected]

Organization name

Central South University

Street address

Renmin Road 139