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Sample GSM1691588 Query DataSets for GSM1691588
Status Public on Aug 29, 2017
Title YL-C-5
Sample type SRA
 
Source name tooth germ
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: apical half of tooth germ
age: post natal day 4
genotype: Control Nfic+/-
Extracted molecule total RNA
Extraction protocol First mandibular molars at PN4 from Nfic-/- and littermate Nfic+/- control mice were dissected out, and the apical half was cut with a fine blade and transferred to RNA stabilization reagent (Qiagen, 76104). Total RNA was extracted with an RNeasy Mini Kit (Qiagen, 74134).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequence, then mapped to mm 10 whole genome using TopHat 2
Read density as Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated following a method of Mortazavi et al 2008, Nature Methods 2008 using an exon model.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file include RPKM values for each wt and mutant mouse is attached as File 1 Normlaized RPKM values
 
Submission date May 19, 2015
Last update date May 15, 2019
Contact name Vasu Punj
E-mail(s) vasupunj@gmail.com
Organization name USC
Street address Biggy Street
City Los Angeles
State/province CA
ZIP/Postal code 90033
Country USA
 
Platform ID GPL19057
Series (1)
GSE69054 An Nfic-Hedgehog Signaling Cascade Regulates Tooth Root Development
Relations
BioSample SAMN03701985
SRA SRX1033801

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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