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Sample GSM981305 Query DataSets for GSM981305
Status Public on Jan 22, 2013
Title Bmp4f/f;Wnt1Cre lower molar
Sample type SRA
Source name molar mesenchyme, lower molar, Bmp4 mutant
Organism Mus musculus
Characteristics strain: mixed background
genotype: Bmp4f/f;Wnt1Cre
age: embryonic day 13.5
tissue: molar mesenchyme (lower molar)
Extracted molecule total RNA
Extraction protocol E13.5 mouse embryo heads were frozen in OCT in liquid nitrogen. The molar mesenchyme was microdissected by LCM after frozen section. Microdissected tissues were frozen at -80℃. Total RNA was extracted by using the RNeasy Micro Kit from Qiagen. cDNA was made by the NuGEN Ovation RNA-Seq v2 Assay. After obtaining the cDNAs, the sequencing libraries were generated by using illumina Nextera DNA Sample Prep kit.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing Illumina offline basecaller v1.9.0.
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to the mm9 whole genome using Bowtie v0.12.7.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009 (PMID 19528076). Implanted in TopHat 1.4.1 using parameters:tophat -G mm9.gtf -o tophat -p 4 -r 0 mm9 reads.fastq. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values (abundance measurements) for each Sample.
Submission date Aug 06, 2012
Last update date May 15, 2019
Contact name Shihai Jia
Organization name Cincinnati Children's Hospital Medical Center
Department Division of Developmental Biology
Lab Rulang Jiang
Street address 3333 Burnet Ave
City Cincinnati
State/province Ohio
ZIP/Postal code 45229
Country USA
Platform ID GPL13112
Series (1)
GSE39918 Next-generation sequencing facilitates quantitative analysis of wild type and Bmp4f/f;Wnt1Cre tooth mesenchyme transcriptomes
SRA SRX174093
BioSample SAMN01103460

Supplementary file Size Download File type/resource
GSM981305_run0142_lane5_index8_13320bmp4mtlower_mouse_cufflinks.txt.gz 718.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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