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Status |
Public on Aug 22, 2022 |
Title |
E13.5 Dental epithelium bio rep2 [E13_E_2] |
Sample type |
SRA |
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Source name |
dental epithelium
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Organism |
Mus musculus |
Characteristics |
tissue: dental epithelium cell type: dental epithelial cells genotype: WT strain: C57BL/6 time point: E13.5
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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)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
Jul 28, 2022 |
Last update date |
Aug 22, 2022 |
Contact name |
Jiawen Chen |
E-mail(s) |
JiaWen960405@126.com
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Organization name |
Southern Medical University
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Street address |
No.1023,South Shatai Road, Baiyun District, Guangzhou, Guangdong, China, 510515
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City |
Guangzhou |
State/province |
Guangdong |
ZIP/Postal code |
510100 |
Country |
China |
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Platform ID |
GPL24247 |
Series (1) |
GSE209968 |
Genome wide identification of potential odontogenic genes involved in the dental epithelium-mesenchymal interaction during early odontogenesis |
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Relations |
BioSample |
SAMN30023688 |
SRA |
SRX16715294 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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