|
| Status |
Public on Jan 29, 2019 |
| Title |
pOKSM |
| Sample type |
SRA |
| |
|
| Source name |
induced neural stem cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6-Pou5f1 x 129X1/SvJ
tissue: Embryonic fibroblast
age: E13.5
genotype: Oct4-CreER x Rosa26-loxSTOPlox-EYFP mouse
|
| Growth protocol |
Mouse embryonic fibroblasts(MEFs) were derived from genetically modifed mouse embryos at embryonic day 13.5 after carefully removing the head and all the internal organs including the spinal cord. Control neural stem cell(cNSCs) were extracted from cerebral cortex of embryo at embryonic day 13.5. induced iNSCs were generated by using polycistronic vector or monocistronic vector. MEFs were infected with lentivirus or retrovirus and induced with neural stem cell medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-Seq experiments with pooled RNA samples extracted from 2-3 biological replicates
Libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Paired-end sequencing reads were mapped to mm10 mouse genome using STAR tool(v2.5.2b).
After mapping, fragments per kilobase million (FPKM) was calculated by Cufflinks (v2.2.1) tool using the following strand-specific Cuffnorm option: --library-type=fr-second strand.
Functional annotation of differentially expressed genes (DEGs) and enrichment analyses were performed using DAVID (v6.8) and Gene Set Enrichment Analysis (GSEA, v2.2.4), respectively, and genes were considered differentially expressed at the fold change > 3 and FPKM > 5. R (v3.3.2) package was used for statistical analyses and scatter plot generation, and RNA-Seq results were visualized using Integrative Genomics Viewer (IGV).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jan 28, 2019 |
| Last update date |
Feb 04, 2019 |
| Contact name |
Chanhyeok Park |
| E-mail(s) |
chpark0729@gmail.com
|
| Organization name |
Konkuk University
|
| Department |
Stem cell and regeneration biotechnology
|
| Lab |
Hong lab
|
| Street address |
120, Neungdong-ro
|
| City |
Seoul |
| ZIP/Postal code |
05066 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE125740 |
Fusion of reprogramming factors alters trajectory of somatic lineage conversion |
|
| Relations |
| BioSample |
SAMN10830149 |
| SRA |
SRX5299572 |
