|
| Status |
Public on Jan 22, 2013 |
| Title |
Bmp4f/f;Wnt1Cre upper molar |
| Sample type |
SRA |
| |
|
| Source name |
molar mesenchyme, upper molar, Bmp4 mutant
|
| Organism |
Mus musculus |
| Characteristics |
strain: mixed background
genotype: Bmp4f/f;Wnt1Cre
age: embryonic day 13.5
tissue: molar mesenchyme (upper 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 |
| E-mail(s) |
shihai.jia@cchmc.org
|
| 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 |
|
| Relations |
| SRA |
SRX174092 |
| BioSample |
SAMN01103459 |
