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Status |
Public on Aug 29, 2017 |
Title |
YL-M-7 |
Sample type |
SRA |
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Source name |
tooth germ
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 tissue: apical half of tooth germ age: post natal day 4 genotype: Nfic-/-
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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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
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Submission date |
May 19, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Vasu Punj |
E-mail(s) |
vasupunj@gmail.com
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Organization name |
USC
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Street address |
Biggy Street
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City |
Los Angeles |
State/province |
CA |
ZIP/Postal code |
90033 |
Country |
USA |
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Platform ID |
GPL19057 |
Series (1) |
GSE69054 |
An Nfic-Hedgehog Signaling Cascade Regulates Tooth Root Development |
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Relations |
BioSample |
SAMN03701990 |
SRA |
SRX1033806 |
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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