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Sample GSM2102845

Query DataSets for GSM2102845

Status

Public on Jun 09, 2017

Title

JF-10

Sample type

SRA

Source name

dental pulp (mouse molar )

Organism

Mus musculus

Characteristics

littermate: 1
strain: Mixed background (C57Bl6/129S6/SvEvTac)
tissue: apical half of tooth germ
age: post natal day 7.5
genotype: control Bmpr1afl/fl

Extracted molecule

total RNA

Extraction protocol

First mandibular molars at PN7.5 from Gli1-CreER;Bmpr1afl/fl and littermate Bmpr1afl/fl control mice were dissected out, and the apical half dental mesenchymel 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 extracted from cells was polyA+ labelled and used to generate libraries following the manufacturer’s protocols (Illumina). The modified cDNA molecules were subjected to sequencing by Illumina Next-Seq 500 system

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: Txt file (File_1_normalized_RPKM_values_Vasu_J_Chai.txt) include RPKM values for each Sample.

Submission date

Mar 31, 2016

Last update date

May 15, 2019

Contact name

Vasu Punj

E-mail(s)

[email protected]

Organization name

USC

Street address

Biggy Street