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Sample GSM4709334 Query DataSets for GSM4709334
Status Public on Aug 31, 2020
Title WT rep2
Sample type SRA
 
Source name Tooth germ
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: wild type
tissue: Tooth germ
age: post natal day 7
Treatment protocol n/a
Growth protocol n/a
Extracted molecule total RNA
Extraction protocol To construct each cDNA library, total RNA in P7 first molars from littermate WT and Gpr115-KO mice was extracted using TRIzol reagent (Invitrogen).
cDNA libraries were produced using a Nextera XT library kit (Illumina), and samples were run on a HiSeq1500 (Illumina) configured for 150 x 150 pair-end reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description total RNA
Data processing Basecalls performed using Illumina’s RTA 2.0.12
Sequenced reads were mapped to GRCm38.vM11 mouse genome using STAR v2.5.2a in  single-pass mode. With the following parameters:  --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.25 --outFilterScoreMinOverLread 0.25 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Genome_build: Custom mm10/GRCm38.vM11+ERCCs
Supplementary_files_format_and_content: Tab delimited files include a raw counts and TMM-normalized expression matrices.
 
Submission date Aug 03, 2020
Last update date Aug 31, 2020
Contact name Yuta Chiba
E-mail(s) yuta.chiba.a8@tohoku.ac.jp
Phone 810227178382
Organization name Tohoku University
Street address 4-1 Seiryo-cho, Aoba-ku
City Sendai
State/province Miyagi
ZIP/Postal code 980-0872
Country Japan
 
Platform ID GPL18480
Series (1)
GSE155641 G-protein coupled receptor Gpr115 (Adgrf4) is required for enamel mineralization mediated by ameloblasts
Relations
BioSample SAMN15716973
SRA SRX8875666

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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