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Sample GSM1691597

Query DataSets for GSM1691597

Status

Public on Aug 29, 2017

Title

YL-M-9

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: 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