|
| Status |
Public on Aug 15, 2017 |
| Title |
Pax9-mt-44-1 |
| Sample type |
SRA |
| |
|
| Source name |
palate shelves
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Palate shelf
age: embryonic day 13.5
genotype: Pax9-/-
treatment: N.A.
|
| Treatment protocol |
the pregnant Pax9+/- females were treated with WAY-262611 daily injection via tail vein from E10.5 to E14
|
| Extracted molecule |
total RNA |
| Extraction protocol |
E13.5 and E14 with or without treatment mouse embryo dissected and put on ice cold PBS, micro-dissect the palate shelves under microscope. Micro-dissected tissues were frozen at -80℃, total RNA was extracted by using RNeasy micro kit from Qiagen.cDNA was made by Illumina TruSeq RNA Sample Prep Kit v2 with oligo(dT) selection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
E13.5 FPKM
|
| Data processing |
Mouse ensembl annotations (build 74) were downloaded and converted to genePred format. Splice junction sequences were generated using USeq’s (v8.8.8) MakeTranscriptome application using a radius of 46. The splice junction sequences were added to the mouse chromosome sequences (mm10) and run through novoindex (v2.8) to create the transcriptome index.
Reads were aligned to the transcriptome index described above using Novoalign (v2.08.03), allowing up to 50 alignments for each read. USeq’s SamTranscriptomeParser application was used to select the best alignment for each read and convert the coordinates of reads aligning to splices back to genomic space.
Read counts for each gene were generated using USeq’s DefinedRegionDifferentialSeq application. These counts were used in DESeq2 to measure the differential expression between each condition.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
|
| |
|
| Submission date |
Nov 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Shihai Jia |
| E-mail(s) |
jiashihai@yahoo.com
|
| Phone |
8018914575
|
| Organization name |
University of Utah
|
| Department |
Department of Neurobiology
|
| Street address |
20 South 2030 East, Room 320 BPRB
|
| City |
Salt Lake City |
| State/province |
ut |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE89603 |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Pax9-/- Palate shelves Transcriptomes |
|
| Relations |
| BioSample |
SAMN05990935 |
| SRA |
SRX2332895 |
