|
Status |
Public on Mar 01, 2016 |
Title |
control rep2 |
Sample type |
SRA |
|
|
Source name |
control_Mandible
|
Organism |
Mus musculus |
Characteristics |
strain background: 129SvEv developmental stage: embryonic day 10.5 genotype/variation: Yapf/f, Tazf/f tissue: mandible
|
Extracted molecule |
polyA RNA |
Extraction protocol |
We dissected E10.5 mandibular tissues from Wnt1Cre Taz and Yap dKO mutant and control embryos in DEPC-treated PBS, then total RNA were extracted and treated for 30 min at 37˚C with RNAse free DNase I (Ambion). Poly(A) RNA was purified with the Micro Poly(A) purist Kit according to the manufacturer’s instructions (Ambion). Purified RNA samples were processed for cDNA synthesis and library preparation following Ion Total RNA-Seq v2 (cat. #4475936) protocol.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Ion Torrent Proton |
|
|
Data processing |
Torrent_Suite 4.0.2 for basecalling with parameters: `BaseCaller --keypass-filter on --phasing-residual-filter=2.0 --trim-qual-cutoff 15 --trim-qual-window-size 30 --trim-adapter-cutoff 16 --num-unfiltered 1000 --calibration-training=100000 --flow-signals-type scaled-residual --max-phasing-levels 2`
Sequenced reads were aligned against mouse genome mm9 using Tmap version 3.0.1 with default RNA-Seq setting `map4`
Gene expression levels were measured by counting numbers of reads in all the exons using HTSeq version 0.5.4p3 with parameters: `htseq-count -m union -s yes -t exon -i gene_symbol`
Differential gene expression was measured using DESeq version 1.16.0
Genome_build: mm9
Supplementary_files_format_and_content: comma-separated values files for raw read counts
Supplementary_files_format_and_content: comma-separated values files for differential gene expressionprofiling
|
|
|
Submission date |
May 27, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Min Zhang |
E-mail(s) |
minzhang5099@gmail.com
|
Organization name |
Baylor College of Medicine
|
Department |
Department of Molecular Physiology
|
Lab |
James F Martin
|
Street address |
One Baylor Plaza Room 504E
|
City |
Houston |
State/province |
Texas |
ZIP/Postal code |
77030 |
Country |
USA |
|
|
Platform ID |
GPL18635 |
Series (1) |
GSE69311 |
Yap and Taz in Neural Crest play a Crucial Role in Smooth Muscle Development |
|
Relations |
BioSample |
SAMN03738166 |
SRA |
SRX1041266 |