GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM6633523

Query DataSets for GSM6633523

Status

Public on Oct 14, 2022

Title

Ctrl_Lung2

Sample type

SRA

Source name

Lung tissue of rats, control group

Organism

Rattus norvegicus

Characteristics

tissue: Lung
treatment: control

Extracted molecule

total RNA

Extraction protocol

RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://0-ccb-jhu-edu.brum.beds.ac.uk/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://0-ccb-jhu-edu.brum.beds.ac.uk/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Rnor_6.0
Assembly: gene expression text files include raw counts and FPKM values for each Sample

Submission date

Oct 12, 2022

Last update date

Oct 18, 2022

Contact name

Ke Gong

E-mail(s)

xzwkgongke@csu.edu.cn

Organization name

The Second Xiangya Hospital of Central South University

Department

cardiovascular surgery