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Sample GSM6411854

Query DataSets for GSM6411854

Status

Public on Aug 22, 2022

Title

E13.5 Dental mesenchymal bio rep1 [E13_M]

Sample type

SRA

Source name

dental mesenchyme

Organism

Mus musculus

Characteristics

tissue: dental mesenchyme
cell type: dental mesenchymal cells
genotype: WT
strain: C57BL/6
time point: E13.5

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.
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)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

we aligned reads of all samples to the Mus musculus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/Mus musculus/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://ccb.jhu.edu/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://ccb.jhu.edu/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.
Assembly: mm10
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

Submission date

Jul 28, 2022

Last update date

Aug 22, 2022

Contact name

Jiawen Chen

E-mail(s)

JiaWen960405@126.com

Organization name

Southern Medical University

Street address

No.1023,South Shatai Road, Baiyun District, Guangzhou, Guangdong, China, 510515