|
| Status |
Public on Nov 09, 2017 |
| Title |
E11.5_Isl1-KO_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Sympathetic ganglion
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Isl1-/-
Stage: embryonic day 11.5
|
| Treatment protocol |
Tissue stored in liquid nitrogen. The ganglia for the same genotype from about 10 embryos with the same genotype were pooled at the time of RNA extraction.
|
| Growth protocol |
Sympathetic ganglion were dissected from E11.5 or E14.5 wild-type and isl1 mutant embryos. To dissect the Sympathetic ganglion of E11.5 embryos，Fluorescence stereoscope was used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the RNeasy Micro kit (Qiagen) following the manufacturer’s instructions. The quality of the resulting RNA was verified by the relative intensity of rRNA bands using a Agilent 2100 Bioanalyzer, and RNA was quantified using a Nanodrop ND-1000 spectrophotometer
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
E11.5_KO_WT_genes_FPKM.txt
|
| Data processing |
mRNA-Seq raw reads were cleaned by removing adaptor sequence and low-quality sequences, aligned to the mouse genome (dm3) using Bowtie/Tophat (v1.3.1) with default parameters.
Uniquely mapped reads were assembled into transcripts guided by reference annotation (FlyBase r5.43) with Cuffdiff (v1.3.0) to calculate gene expression levels which measured as Fragment Per Kilobase per Million mapped fragments (FPKM) and identify differentially expressed genes with FDR < 0.05.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene which FPKM large than 1 at least in one sample.
|
| |
|
| Submission date |
Jan 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Youqiong Ye |
| E-mail(s) |
youqye@gmail.com
|
| Phone |
+8613661565591
|
| Organization name |
Shanghai Jiao Tong University School of Medicine
|
| Street address |
280 Chongqing south road
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE93306 |
Genome-wide mRNA expression analyses revealed dysregulation of genes important for sympathetic neuron development in isl1 cko and hypomorphic mutant embryos. |
| GSE93308 |
Genome-wide studies of sympathetic neuron development |
|
| Relations |
| BioSample |
SAMN06212474 |
| SRA |
SRX2480235 |
