|
| Status |
Public on Jul 16, 2019 |
| Title |
WT_3 |
| Sample type |
SRA |
| |
|
| Source name |
primary neurosphere derived from dorsal cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: primary neurosphere derived from dorsal cortex
strain: C57BL/6
age: E14.5
genotype: WT
|
| Growth protocol |
NPCs were isolated from E14.5 mice by dissection of the lateral walls of the lateral ventricles and digested into single cell suspension with Accutase (Sigma). Cells were cultured in DMEM/F12 proliferation medium supplemented with 2% B27 supplement, 20 ng/ml EGF, 20 ng/ml bFGF and 0.2% BSA for proliferation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Neurosphere RNA isolated from the 6th day culturing NPCs dissected from E14.5 mice.
A total amount of 3 µg RNAper sample was used as input material for the RNAsample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential gene expression analysis was performed through DESeq2 (v1.16.1)
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
|
| |
|
| Submission date |
Jun 27, 2019 |
| Last update date |
Jul 16, 2019 |
| Contact name |
Xiaozhong Peng |
| E-mail(s) |
pengxiaozhong@pumc.edu.cn
|
| Phone |
86 69156434
|
| Organization name |
Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College
|
| Department |
Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences
|
| Lab |
Lab of Xiaozhong Peng
|
| Street address |
No.5, Dongdan Santiao, Dongcheng District
|
| City |
Beijing |
| ZIP/Postal code |
100005 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE120988 |
COMPASS Family Histone Methyltransferase ASH2L Mediates Corticogenesis via Transcriptional Regulation of Wnt Signaling |
| GSE133413 |
COMPASS Family Histone Methyltransferase ASH2L Mediates Corticogenesis via Transcriptional Regulation of Wnt Signaling [RNA-Seq 2] |
|
| Relations |
| BioSample |
SAMN12147660 |
| SRA |
SRX6370213 |
