|
| Status |
Public on Dec 10, 2012 |
| Title |
HPRT knockdown SNM (8 day) |
| Sample type |
SRA |
| |
|
| Source name |
D3 embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: spherical neural mass derived form D3 embryonic stem cells
strain: 129s2/SvPas
development: neuronal differentiation
treatment: infected by retrovirus with shRNA against HPRT
differentiation day: 8
|
| Treatment protocol |
HPRT knockdown cells were infected by retrovirus with shRNA against HPRT and control cells were infected by retrovirus with shRNA against luciferase.
|
| Growth protocol |
The D3 embryonic stem cells were maintained on primary mouse embryo fibroblast feeder cells in ES medium consisting of DMEM/F12 medium, 20% (v/v) KOSR, 1 mM of L-glutamine, 4ng/ml of bFGF, 1,000 U/ml of LIF, 1% (v/v) NEAA, 50 U/ml of penicillin, 50 ug/ml of streptomycin and 0.1 mM of 2-mercaptoethanol. All cell cultrue and neuronal differentiations were carried out in established cell culture conditions (5% CO2, 37 °C). Dopaminergic neuronal differentiation of SNMs derived from D3 embryonic stem cells was carried out according to the protocol published Cho et al. (Nature Protocols 2008, 3, 1888 - 1894.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from HPRT knockdown and control cells were purified by Rneasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer's instruction. The total RNA of each SNM sample was obtained from the independently replicated cultures.
Library preparation was performed with TruSeq RNA Sample Preparation Kit v2 of Illumina, and the prepared libraries were validated and quantified with Agilent bionalyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2.
RNA-Seq reads were aligned to the mm9 mouse genome using ELAND alignment algorithm.
Aligned data were imported to Avadis NGS 1.3.1 (Strand Scientific Intelligence), and the reads were filtered by Illumina tile plot filter.
The normalization algorithm was DESeq, and the differential gene expression (≥1.5 or ≥ 2.0 fold) during the neuronal differentiation of HPRT knockdown and control SNMs was selected.
The biological significance of the altered gene expressions were interpreted by GO and signaling pathway analyses using Avadis NGS and Panther Classification System.
Genome_build: mm9
|
| |
|
| Submission date |
Dec 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Tae Hyuk Kang |
| E-mail(s) |
t2kang@ucsd.edu
|
| Phone |
853-534-1419
|
| Fax |
858-534-1422
|
| Organization name |
University of California, San Diego
|
| Department |
Pediatrics
|
| Lab |
Dr. Friedmann's laboratory
|
| Street address |
9500 Gilman Drive # 0634
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE42662 |
UC San Diego Friedmann Kang Neuronal Differentiation DSD3 SNM |
|
| Relations |
| SRA |
SRX208083 |
| BioSample |
SAMN01822117 |
